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10/2020 Fang Bai
An, XL, et al. 2020. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.2010255117
   Molecular regulation of ZmMs7 required for maize male fertility and development of a dominant male-sterility system in multiple species

Developing a male-sterility system that is effective in multiple species is essential for hybrid seed production in different plants, especially for plants without cloned male-sterility genes. Here, we identified the transcriptional regulation mechanism for maize male-sterility gene ZmMs7 and thereby developed a dominant male-sterility system that was proved to be effective in maize, rice, and Arabidopsis. Compared with current male-sterility systems, this system has potential advantages, e.g., utilization of a single transgene cassette, high stability of male sterility under different genetic backgrounds, and producing fluorescent transgenic and normal color nontransgenic F1 hybrid seeds which can be used flexibly in different countries where transgenic crop cultivation is prohibited or allowed. Therefore, it is a simple, cost-effective, and multiple-crop-applicable biotechnology.

ZmMs7 encodes a PHD-finger transcription factor regulating anther and pollen development. ZmMs7 mutant is male-sterility, which is maintained and propagated as a female parent line for hybrid seed production. In this paper, An et al. showed that ZmMs7 is specifically expressed in maize anthers at tetrad and free haploid microspore stages from stages 8b to 10 and peaked at stage 9. Through Y2H, CO-IP assays, and BIFC, the authors found that ZmMs7 formed a complex with other transcription factors during the tapetum development and pollen exine formation. Both in vitro of transactivation assay and in vivo of chromatin immune-precipitation quantitative PCR (ChIP-qPCR) assay demonstrated that ZmMs7-NF-Y complexes directly activated target gene ZmMT2C, a reported GMS gene in rice and Arabidopsis. In this study, the authors further developed an applicable dominant male sterility (DMS) line p5126-ZmMs7 and evaluated the stability by crossing the p5126-ZmMs7M-01 line with 392 maize inbred lines with broad genetic diversity. Both the recessive mutant line of ms7-6007 and DMS line p5126-ZmMs7M-01 are stable male sterility lines and have no obvious negative effects on maize heterosis and field production. Their work is significantly important for exploring the molecular mechanism of male-sterility and providing a novel tool for modern hybrid crop breeding. Fang Bai, 2020

10/2020 Mohammad Arif Ashraf
Marcon, C, et al. 2020. Plant Physiol. 0:doi: 10.1104/pp.20.00478
   BonnMu: a sequence-indexed resource of transposon-induced maize mutations for functional genomics studies

For the maize community, some of the major resources are mutational insertion libraries such as UniformMU, ChinaMu, and Mu-Illumina. In a recent Plant Physiology paper, Frank Hochholdinger���s group from University of Bonn described another Mutator(Mu)-transposon insertion sequence-indexed library in B73 background, named as BonnMu. In the BonnMu, they have detected total 2,25,936 insertion sites, among them 41,086 sites are germinal Mu insertions, and these insertion sites cover 37% annotated genes based on B73v4 genome. The BonnMu is already incorporated into the maize Genetics and Genomics database ( along with their insertion site information and phenotypic images. Arif Ashraf, 2020

For the maize community, some of the major resources are mutational insertion libraries such as UniformMU, ChinaMu, and Mu-Illumina. In a recent Plant Physiology paper, Frank Hochholdinger���s group from University of Bonn described another Mutator(Mu)-transposon insertion sequence-indexed library in B73 background, named as BonnMu. In the BonnMu, they have detected total 2,25,936 insertion sites, among them 41,086 sites are germinal Mu insertions, and these insertion sites cover 37% annotated genes based on B73v4 genome. The BonnMu is already incorporated into the maize Genetics and Genomics database ( along with their insertion site information and phenotypic images. Arif Ashraf, 2020

For the maize community, some of the major resources are mutational insertion libraries such as UniformMU, ChinaMu, and Mu-Illumina. In a recent Plant Physiology paper, Frank Hochholdinger's group from University of Bonn described another Mutator(Mu)-transposon insertion sequence-indexed library in B73 background, named as BonnMu. In the BonnMu, they have detected total 2,25,936 insertion sites, among them 41,086 sites are germinal Mu insertions, and these insertion sites cover 37% annotated genes based on B73v4 genome. The BonnMu is already incorporated into the maize Genetics and Genomics database ( along with their insertion site information and phenotypic images.

10/2020 Samantha Snodgrass
Matonyei, TK, et al. 2020. Sci. Rep.. 10:7320
   Aluminum tolerance mechanisms in Kenyan maize germplasm are independent from the citrate transporter ZmMATE1

Matonyei et al 2020 found Kenyan landraces have a different mechanism of Aluminum tolerance than the Brazilian line Cateto Al237. They created a mapping population with the Al-tolerant 203B-14 and Al-sensitive SCH3 Kenyan lines, which have similar respective Al-tolerances as the Brazilian mapping population founders Cateto Al237 and L53. Five Al tolerance QTLs were identified. Taken with the QTL main effects and four epistatic interactions, these explained ~51% of the Al-tolerance. ZmMATE1 was not among the five QTL even though it is a major contributor of aluminum tolerance in Brazilian lines. Expression levels confirmed ZmMATE1 is not induced by Al in Kenyan roots as it is in the Brazilian lines. Mayonyei and colleagues found several interesting candidates underlying the QTLs, including ZmMATE3, ZmNrat1, ZmWRKY, and ZmART1. Taken together, this suggests an alternative mechanism of aluminum tolerance has arisen in Kenyan germplasm compared to Brazilian germplasm. Samantha Snodegrass, 2020

10/2020 Marcio Resende
Costa-Neto, G; Fritsche-Neto, R; Crossa, J. 2020. Heredity. 0:Epub
   Nonlinear kernels, dominance, and envirotyping data increase the accuracy of genome-based prediction in multi-environment trials

Nonlinear kernels, dominance, and envirotyping data increase the accuracy of genome-based prediction in multi-environment trials. Costa-Neto et al. explored the integration of genomics and nongenomic sources of variation in genomic prediction models evaluated in two multi-environment maize trials. The authors compared prediction models using different kernels including an implementation of an arc-cosine kernel defined by a covariance matrix that emulates a deep-learning model with one hidden layer and a large number of neurons. Environmental variables were incorporated through a reaction-norm modeling. The Gaussian and Arc-cosine kernels outperformed conventional GBLUP approached in reducing the computational time, and increased the prediction ability for all testing scenarios in tropical maize. The authors further discuss application of the different genomic prediction models to capture non additive affects. Marcio Resende, 2020

10/2020 Samuel Leiboff
Lai, X, et al. 2020. BMC Genomics. 21:428
   Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs

Orthologous relations with other species of the following models: GRMZM2G175227   GRMZM2G175265   GRMZM2G474769 GRMZM2G014902 GRMZM2G145041 GRMZM2G135052 GRMZM2G170148 GRMZM2G057408 GRMZM5G833032 GRMZM2G118693 GRMZM2G029850 GRMZM2G170322 GRMZM2G421256 GRMZM2G115070 GRMZM2G415077 GRMZM2G148453 GRMZM2G020081 GRMZM2G005732 GRMZM2G033962 GRMZM2G488465   GRMZM2G013913 GRMZM2G135446 GRMZM2G095727 GRMZM2G179024 GRMZM2G367834 GRMZM2G107101 GRMZM5G844173 GRMZM2G045275 AC233870.1_FG003 GRMZM2G382774 GRMZM2G359322 GRMZM5G877647 GRMZM2G025646 GRMZM2G067702 GRMZM2G115914 GRMZM2G113244 GRMZM2G147800 GRMZM2G166147 GRMZM2G106363 GRMZM2G107945

Most life on earth uses an environmentally-entrained rhythmic rise and fall of transcripts / proteins to define a circadian clock. Plants use these diurnal rhythms to match important processes like photosynthesis, starch metabolism, and growth to optimal phases of the day. Much of what we know about the plant circadian clock comes from work in Arabidopsis thaliana. And although there is evidence that the core proteins of the circadian clock are conserved across plant species, it is unclear if they fluctuate similarly in all species or how the global pattern of rhythmic genes varies between species. Lai and Bendix et al., used a diurnal RNAseq timecourse of maize, sorghum, and foxtail millet (Setaria italica) to demonstrate that the homologues of known clock genes do indeed fluctuate over a 24 hr period, mostly as expected. Around 17.5 thousand maize transcripts followed what looked like a diurnal pattern, with 86% of those fitting a 24-hour rhythm. Intriguingly, some clock transcripts in maize, with an extra whole genome duplication compared to sorghum and foxtail millet, tended to fluctuate with a reduced amplitude, or smaller change in FPKM compared to the other species, suggesting that there might be intriguing dosage requirements split between maize paralogs that do not exist in other species. They used carefully-optimized clustering then promoter motif searches to identify new rhythmic diurnal gene clusters and the sequence motifs that might drive them. This careful approach identified known circadian clock binding sequences as well as a wealth of new putative sequences across species. By combining the analysis of multiple species, Lai and Bendix et al. have uncovered a whole host of new diurnally-regulated genes and potentially-conserved regulatory information that drives them. Sam Leiboff, 2020

BioProject at the National Center for Biotechnology Information under accession number PRJNA616061 (

9/2020 Mohammad Arif Ashraf
Li, CB, et al. 2020. Plant Cell. 0:doi: 10.1105/tpc.20.00352
   A SnRK1-ZmRFWD3-Opaque2 signaling axis regulates diurnal nitrogen accumulation in maize seeds

Nitrogen assimilation in developing maize seeds is regulated by the SnRK1-ZmRFWD3-O2 signaling axis,which is responsive to diurnal sucrose concentrations.

Li et al. identified Opaque2 (O2) interacting protein, which contains both C3HC4 zinc finger RING-type and WD40/YVTN repeat domain and named as ZmRFWD3 based on its domain organization. Between these two domains, WD40 repeat domain facilitates the interaction with O2 and RING domain demonstrates E3 ubiquitin ligase activity on O2 at Lys-235. ZmRFWD3-mediated ubiquitination process alters subcellular localization of O2. In wild-type, O2 localizes to the nucleus, whereas it has cytosol-specific localization in zmrfwd3-mu1 seeds. Furthermore, authors have found that ZmRFWD3 -mediated ubiquitination of O2 at Lys-235 induces its interaction with ZmIMP1, maize importin1 protein has capacity to bind with nuclear localization signal (NLS), and consequently demonstrates nuclear prominent localization. ZmRFWD3 is not only facilitate post-translational modification such as ubiquitination, but it is also subjected to post-translational modification - ZmSnRK1α2 phosphorylates ZmRFWD3 at serine-479 and induces the degradation through 26S proteasome pathway. Finally, authors demonstrated diurnal rhythms controls the sucrose concentration and consequently sucrose concentration regulates the protein level of ZmRFWD3 and subcellular distribution of O2 protein. Arif Ashraf, 2020

9/2020 Samantha Snodgrass
Burgess, D; Li, H; Zhao, M; Kim, SY; Lisch, D. 2020. Genetics. 215:379-391
   Silencing of Mutator elements in maize involves distinct populations of small RNAs and distinct patterns of DNA methylation

Transposable elements (TEs) are a ubiquitous feature of plant genomes. Because of the threat they post to genome integrity, most TEs are epigenetically silenced. However, even closely related plant species often have dramatically different populations of TEs, suggesting periodic rounds of activity andsilencing. Here we show that the process of de novomethylationof an active element in maize involves two distinct pathways, one of whichis directly implicated in causing epigenetic silencing and one of which is the result 43of that silencing.

Burgess et al 2020 dissect the mechanism by which the 3' and 5' TIRA section of a MuDR transposable element is methylated. They discovered that these two ends of the TIRA (Terminal Inverted Repeat A) are methylated by different means using a mutant MuDR-d107 that has a deletion in the mudrA transposase gene but is otherwise identical to an active MuDR element. The researchers show Muk, a trans-acting regulating locus of MuDR, heritably silences MuDR elements via small RNAs created from Muk hairpin transcripts. The hairpin matches to the mudrA transposase sequence which in turn trigger de novo methylation of the 3' TIRA. The 5' TIRA was shown to be methylated by more common "background" small RNAs with some mismatch. They also demonstrate the mudrB is silenced indirectly by Muk given divergence of the TIRA and TIRB sequence. Samantha Snodgrass, 2020

9/2020 Fang Bai
Teng, C, et al. 2020. Nature communications. 11:2912
   Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize

There are five DICER-like (DCL) proteins that are involved in the small RNAs biogenesis in the flowering plants. Teng et al. generated and characterized dcl5 mutants in maize to study the function of the DCL5. Using the scanning electron microscope and the transmission electron microscope, the null mutants of dcl5 showed the defects in tapetal cell differentiation, which caused the male-sterile phenotype. The authors found few or no 24-nt phasiRNAs produced in null dcl5 mutants, which indicated that DCL5 is required for 24-nt phasiRNA biogenesis. Furthermore, they observed that the anther fertility in dcl5 mutants are temperature-sensitive. Their work is significant to report the roles of DCL5 in regulating male fertility through 24-nt phasiRNA and environmental factors. Fang Bai 2020

9/2020 Marcio Resende
Kolkman, JM, et al. 2020. G3. 0:doi: 10.1534/g3.120.401500
   Maize introgression library provides evidence for the involvement of liguleless1 in resistance to northern leaf blight

The authors characterized 412 BC5F4 near-isogenic lines originated from 18 diverse donor parents and backcrossed into B73. The population was genotyped with GBS and characterized for Northern Corn Leaf Blight resistance after inoculation with Setosphaeria turcica isolate NY001 (race 1). The experiment was evaluated in four environments and the data was analyzed to identify pairwise differences between NILs and the recurrent parent B73. Association mapping narrowed one QTL to a 1.3 Mb interval flanked by mechanosensitive channel of small conductase (GRMZM2G005996) and trehalose-6-phosphate phosphatase 6 (GRMZM2G112830). A second QTL was mapped to chromosome 2, immediately downstream of the liguleless1 gene (lg1, GRMZM2G036297). Two independently-derived mutant alleles of lg1 inoculated with S. turcica showed increased susceptibility to northern corn leaf blight. Marcio Resende, 2020

8/2020 Samantha Snodgrass
Liu, HJ et al. 2020. Plant Biotechnol J 18:185-194
   Genome-wide identification and analysis of heterotic loci in three maize hybrids

Liu et al used 3 hybrid-parent trios to map loci associated with heterosis for 19 traits. They resequenced the 6 parental lines to 30x coverage and thousands of F2 individuals to 0.2x coverage using Illumina 150-bp paired-end reads. With this genetic information and the 19 trait data, they were able to estimate dominance-additive effects and map between 158 and 256 QTL per population. Their findings support the main action of heterosis is through dominance instead of overdominance in maize. Interestingly, 76 of the identified QTL overlapped between populations for the same trait, even though these lines span Chinese and USA public breeding programs. Liu and colleagues chose 17 identified QTL to validate in a follow up study and confirmed 15. Of note, they found a large effect QTL capturing the ub3 gene that had a large effect on heterosis of tassel branch number and kernel yield per ear. Samantha Snodgrass, 2020

The DNA sequencing data of the six parental lines are deposited in the European Nucleotide Archive under accession numbers PRJEB30082,

8/2020 Fang Bai
Teng, C, et al. 2020. Nature communications. 11:2912
   Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize

There are five DICER-like (DCL) proteins that are involved in the small RNAs biogenesis in the flowering plants. Teng et al. generated and characterized dcl5 mutants in maize to study the function of the DCL5. Using the scanning electron microscope and the transmission electron microscope, the null mutants of dcl5 showed the defects in tapetal cell differentiation, which caused the male-sterile phenotype. The authors found few or no 24-nt phasiRNAs produced in null dcl5 mutants, which indicated that DCL5 is required for 24-nt phasiRNA biogenesis. Furthermore, they observed that the anther fertility in dcl5 mutants are temperature-sensitive. Their work is significant to report the roles of DCL5 in regulating male fertility through 24-nt phasiRNA and environmental factors. Fang Bai 2020

8/2020 Marcio Resende
Castorina, G, et al. 2020. Plant Physiol. 0:doi: 10.1104/pp.20.00322
   Drought-responsive ZmFDL1/MYB94 regulates cuticle biosynthesis and cuticle-dependent leaf permeability

The MYB transcription factor FUSED LEAVES1 regulates and the abscisic acid influences cuticle biosynthesis and cuticle-mediated drought response during the juvenile phase of maize plant growth.

This work studied cuticle deposition and cuticle-dependent leaf permeability during the juvenile phase of plant development in maize. Cuticle constitutes a barrier against damages caused by abiotic and biotic stresses. The authors identify a MYB transcription factor (ZmFUSED LEAVES 1 (FDL1)/MYB94) that affects cuticle deposition and leaf permeability. Mutant seedlings for the gene (fdl1-1) showed altered cutin and wax biosynthesis and deposition at the coleoptile stage. Reduction in cutin content was mainly due to decreases in w-hydroxy fatty acids and polyhydroxy-fatty acids. Homozygous mutants show irregular coleoptile opening and presence of fusions between coleoptile and first leaf. The decrease in epicuticular wax was mainly due to reduction in primary long-chain alcohols, which represent the major components of maize seedling waxes. The authors then looked at RNA-seq in the mutant and identified enrichment of differentially expressed genes involved in lipid metabolism. The transcriptome was also used to propose a pathway for cuticle biosynthesis in maize. The authors further investigated the role of cuticle and cuticle-related genes in mediating water stress response and show that drought and ABA affect cuticular permeability and the expression of FDL1/MYB94. Marcio Resende, 2020

8/2020 Mohammad Arif Ashraf
Martinez, P, et al. 2020. J Cell Biol. 219:e201907184
   TANGLED1 mediates microtubule interactions that may promote division plane positioning in maize

During plant cell division, the preprophase band acts as an indicator for the future division site. As microtubules provide the dynamic framework during mitosis, it constitutes preprophase band (PPB), metaphase spindle, and phragmoplast. As cell division progresses, the preprophase band is disassembled in metaphase and the phragmoplast is assembled during telophase. Maize mutant tangled1 (tan1) fails to maintain the division plane orientation and results in division plane defects for symmetric and asymmetric cell division. In this study, Martinez et al. demonstrated that TAN1 binds to microtubules and does not alter the microtubule dynamics based on in vitro studies. Additionally, they have shown that TAN1 interacts with microtubules to maintain spindle organization and orientation. Altogether, this study provided an idea about TAN1-mediated microtubule organization and phragmoplast guidance. Arif Ashraf, 2020

8/2020 MaizeGDB Staff
. 2020. Nature Genetics. 52:754-758
   Guidelines for human gene nomenclature

If each maize gene had a unique name, or "globally unique persistent identifier", it would be easier to communicate and aggregate information about each gene. A good nomenclature system has two components: community agreed on guidelines and a clearing house authority through which all proposed names are reviewed to insure uniqueness. In the genomics era, gene nomenclature systems in many fields are no longer rigorously followed, leading to difficulties. Researchers who work on human genes have an advantage in the HUGO consortium- where, with lots of funding, a dedicated group of scientists work to ensure unique human gene names. Their nomenclature is also being extended to other vertebrates, thus creating a consistent gene nomenclature for a large clade. In this comment, they outline their strategies. MaizeGDB, 2020

7/2020 Mohammad Arif Ashraf
Muszynski, MG, et al. 2020. Plant Cell. 0:doi; 10.1105/tpc.19.00677
   The maize Hairy Sheath Frayed1 (Hsf1) mutant alters leaf patterning through increased cytokinin signaling

In this study authors have identified maize leaf patterning mutant Hairy Sheath Frayed1 (Hsf1). Among five Hsf1 alleles, a transition mutation, causes missense mutation in the highly conserved amino acid, was found in the CHASE (Cyclase/Histidine-kinase-associated sensory) domain of cytokinin receptor, ZmHK1 (Zea mays Histidine Kinase1). And this missense mutation leads to gain-of-function of ZmHK1, which acts as constitutively active cytokinin signaling. Interestingly, exogenous application of cytokinin, 6-benzylaminopurine (BA), demonstrates Hsf1-like phenotype. Consistent with this observation, authors have found that cytokinin-responsive genes, such as ZmRR2, ZmRR3; expression is induced in Hsf1/+ mutants and indicates the downstream target from cytokinin signaling. Double mutant of Hsf1 and zmrr3/abph1, has synergistic phenotype, which clearly suggests the functional role of downstream cytokinin signaling components. Arif Ashraf, 2020

7/2020 Damon Lisch
Fang Bai
Sun, YH, et al. 2020. Genome Biol. 21:143
   3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize

We are just at the point where we can begin to ask big questions in maize about the relationships between large scale chromatin changes, gene expression and differentiation. HC, which detects long range interactions between regulatory regions in genes, ATAC, which detects open chromatin, ChIP, which detects chromatin modifications and RNAseq are used to examine changes in homologous structures (ear and tassel) in maize. It's a nice model because it illustrates how changes in gene expression and structure can results in dramatically different structures variations in single original pathway. The data set is very useful. Reassuringly, but perhaps not surprisingly, they found clear connections between differential gene expression and associations with putative regulatory regions, and chromatin marks are distributed in the manner one might expect. In addition, many of those informative SNPs are associated with extrachromosomal regulatory regions. I would have loved to see an analysis of the role of conserved non-coding regions. A direct comparisons of sorghum would be fascinating, as would an analysis of sets of genes from each of the two duplicated subgenomes of maize. Further, in addition to showing that the genes that we know are regulated in particular ways are in fact regulated in those ways, it would be nice to see some surprises. Presumably, data sets like these will eventually make us fundamentally re-think some of our ideas about gene regulation based on those surprises. But that is asking a lot. As it is, this will be an invaluable resource for anyone interested in gene regulation, differentiation and evolution of genetic pathways. Damon Lisch, 2020

Tassel and ear are the male and female inflorescences in maize, respectively. To explore the 3D view of the genome coordinates the cis- and trans-regulation in open chromatin regions (OCRs) during the maize tassel and ear development, Sun et al. (2020) identified 56,055 OCRs in 2-4mm of ear primordia and 52,633 OCRs (OCRs) in developing tassel primordia using ATAC-seq. The authors then demonstrated that the dynamics of local OCRs and the histone modifications are correlated to the differential expression of genes (DEGs) in ear and tassel. Using ChIP-seq and RNA-seq datasets, Sun et al. found that the specific binding of the TFs with the OCRs of the target genes drove the DEGs expression between the ear and tassel. They next identified 15,084 and 13,178 topologically associating domains (TADs) at 5 KB resolution in ear and tassel, respectively, and provided high-resolution chromatin interaction maps for ear and tassel primordia. The authors further identified 42,300 and 28,748 chromatin loops connecting OCRs and genes in ear and tassel and found a positive correlation between the number of loops and gene expression levels. In addition, Sun et al. investigated that the agronomic trait-associated intergenic SNPs can be connected to potential target genes via loops that may control the phenotypic of ear and tassel. Their findings of the chromatin loops and epigenetic states of OCRs in tissue-specific gene expression are significant and help to understand the morphological and developmental diversity of the ear and tassel. Fang Bai 2020

7/2020 Marcio Resende
Cao, YB, et al. 2020. Nature communications. 11:186
   Natural variation of an EF-hand Ca2+-binding-protein coding gene confers saline-alkaline tolerance in maize

The authors in this study used GWAS in 419 maize inbred lines and identified a candidate gene ZmNSA1 (GRMZM2G000397) associated with shoot Na+ content and saline-alkaline tolerance in maize. This candidate gene has orthologues in other plant species, but their function is unknown. A mu insertion in ZmNSA1 indicated undetectable differences under control condition, but plants were larger and conferred lower shoot Na+ content than that of W22 under NaHCO3 (100mM) condition. Conversely, plants over expressing ZmNSA1 were smaller and conferred greater shoot Na+ contents than wild type under NaHCO3 condition. The authors further demonstrate that this gene is involved in the regulation of root Na+ efflux, but is unlikely associated with the regulation of Na+ uptake. The protein is localized in the cytosol and NaHCO3 treatment triggers the degradation of ZmNSA1 protein via the 26S proteasome pathway. A working model for the salinity tolerance controlled by ZmNSA1 is proposed. Marcio Resende, 2020

7/2020 Samantha Snodgrass
Burgess, D; Li, H; Zhao, M; Kim, SY; Lisch, D. 2020. Genetics. 215:379-391
   Silencing of Mutator elements in maize involves distinct populations of small RNAs and distinct patterns of DNA methylation

Transposable elements (TEs) are a ubiquitous feature of plant genomes. Because of the threat they post to genome integrity, most TEs are epigenetically silenced. However, even closely related plant species often have dramatically different populations of TEs, suggesting periodic rounds of activity andsilencing. Here we show that the process of de novomethylationof an active element in maize involves two distinct pathways, one of whichis directly implicated in causing epigenetic silencing and one of which is the result 43of that silencing.

Burgess et al 2020 dissect the mechanism by which the 3' and 5' TIRA section of a MuDR transposable element is methylated. They discovered that these two ends of the TIRA (Terminal Inverted Repeat A) are methylated by different means using a mutant MuDR-d107 that has a deletion in the mudrA transposase gene but is otherwise identical to an active MuDR element. The researchers show Muk, a trans-acting regulating locus of MuDR, heritably silences MuDR elements via small RNAs created from Muk hairpin transcripts. The hairpin matches to the mudrA transposase sequence which in turn trigger de novo methylation of the 3' TIRA. The 5' TIRA was shown to be methylated by more common "background" small RNAs with some mismatch. They also demonstrate the mudrB is silenced indirectly by Muk given divergence of the TIRA and TIRB sequence. Samantha Snodgrass, 2020

7/2020 Samantha Snodgrass
Burgess, D; Li, H; Zhao, M; Kim, SY; Lisch, D. 2020. Genetics. 215:379-391
   Silencing of Mutator elements in maize involves distinct populations of small RNAs and distinct patterns of DNA methylation

Transposable elements (TEs) are a ubiquitous feature of plant genomes. Because of the threat they post to genome integrity, most TEs are epigenetically silenced. However, even closely related plant species often have dramatically different populations of TEs, suggesting periodic rounds of activity andsilencing. Here we show that the process of de novomethylationof an active element in maize involves two distinct pathways, one of whichis directly implicated in causing epigenetic silencing and one of which is the result 43of that silencing.

Burgess et al 2020 dissect the mechanism by which the 3' and 5' TIRA section of a MuDR transposable element is methylated. They discovered that these two ends of the TIRA (Terminal Inverted Repeat A) are methylated by different means using a mutant MuDR-d107 that has a deletion in the mudrA transposase gene but is otherwise identical to an active MuDR element. The researchers show Muk, a trans-acting regulating locus of MuDR, heritably silences MuDR elements via small RNAs created from Muk hairpin transcripts. The hairpin matches to the mudrA transposase sequence which in turn trigger de novo methylation of the 3' TIRA. The 5' TIRA was shown to be methylated by more common "background" small RNAs with some mismatch. They also demonstrate the mudrB is silenced indirectly by Muk given divergence of the TIRA and TIRB sequence. Samantha Snodgrass, 2020

7/2020 Fang Bai
Qiao, P, et al. 2020. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.2004945117
   Transcriptomic network analyses shed light on the regulation of cuticle development in maize leaves

Plant cuticles provide barriers to water loss and arose as aquatic plants adapted to the dry terrestrial environment. The cuticle components, waxes and the fatty acid-based polymer cutin, are synthesized in the plant epidermis, exported across the cell wall, and deposited on the plant surface. This study suggests a role for PHYTOCHROME light receptors during cuticle development in leaves of maize and moss, diverse species that are separated by more than 400 million y of land plant evolution. We hypothesize that phytochrome-mediated light signaling contributed to the evolution of cuticles in land plants.

Plant cuticle is a layer comprised of waxes and cutins that are hydrophobic barriers on the epidermis of the leaves to prevent water loss. To explore the genetic and biochemical reasons of the plant cuticle deposition on the land plant leaf, Qiao et al. (2020) did the laser micro-dissect both L1 and L2 derived epidermal cells from the expanding leaf8 of B73 along the light-shielded proximal intervals to light-exposed distal regions and analyzed the transcriptomic data. They identified the photoreceptors PHYA1 and PHYB1 in maize, which regulate the cuticle accumulation, and showed that the mutants of phy altered the cuticle composition during the leaf development. The authors also explored the relationship between the phytochrome-mediated light signaling and the evolution of cuticles in land plants. Fang Bai 2020

7/2020 Samuel Leiboff
Ramos Baez, R, et al. 2020. Plant Physiol. 0:doi: 10.1104/pp.19.01475
   A synthetic approach allows rapid characterization of the maize nuclear auxin response circuit

One of the most vexing things about the phytohoromone auxin is its role in almost every aspect plant growth and development. The breadth of these responses is often attributed to the multitude of auxin-response transcription factors, their repressors, and other components of the regulatory machinery. The maize genome encodes dozens of these potentially interacting, probably redundant auxin-related proteins, leading to a combinatorial complexity that has limited the mechanistic study of auxin. Baez et al address this complexity by rebuilding a synthetic auxin signaling circuit in bakers yeast (Saccharomyces cerevisiae). In their reconstituted auxin response pathway, Baez et al control the exact combination of auxin sensor, repressor, and transcription factor over multiple auxin concentrations. They use this system to compare an impressive variety of maize auxin proteins, including those cloned with mutant phenotypes and those that are presumed genetically redundant. By systematically comparing maize or Arabidopsis proteins, Baez et al show that maize auxin response factors (ARFs) and AUX/IAAs are more repressive than those from Arabidopsis, while maize TIR/ABPs are more auxin sensitive (possibly active in the absence of auxin), suggesting that although the auxin signaling machinery is conserved between species, it might be 'tuned' to respond differently. Synthetic systems like the one reported by Baez et al are an intriguing way of studying gene regulatory circuits outside the noisy context of the plant cell. Engineered systems open the possibility of comparing mechanistic gene function across species, potentially revealing unique responses to ancient, conserved stimuli, like auxin. Sam Leiboff, 2020

6/2020 Mohammad Arif Ashraf
Ding, L, et al. 2020. Plant Physiol. 0:doi; 10.1104/pp.19.01183
   Modification of the expression of the aquaporin ZmPIP2;5 affects water relations and plant growth

Aquaporins, also known as plasma membrane intrinsic proteins (PIP), are a large group of transporters that facilitate water transport through plasma membranes. Within this large family of transporter, maize root preferentially has higher expression of PIP2;5 protein. Authors in this article took the advantage of highly expressed PIP2;5 to understand how water regulates growth in maize at both cellular and whole plant level. For this purpose, they have used overexpressed and knock-out lines of PIP2;5. In this work, they have used the MECHA model, which can calculate water flow radially at subcellular level in root. In root, they have found that PIP2;5 knock-out line has decreased hydraulic conductivity, but over-expression line does not demonstrate contrasting activity. Using the MECHA model, they have explained the puzzle with a possible explanation that plasma membrane permeability is not uniform radially in the root or specific cell layers are saturated with PIP2;5 in the overexpression line. The explanation is further supported by the hydraulic study in the leaf. Because, compared to root, PIP2;5 is less expressed in the leaf and in that case PIP2;5 saturation would not be an issue. Consistent with this idea, PIP2;5 over-expression line has higher hydraulic conductivity in the leaf. The knowledge from this article can be used further to explore the role of PIP2;5 or water conductivity at various environmental conditions. Arif Ashraf, 2020

6/2020 Marcio Resende
Holland, J et al. 2020. Crop Sci pp.doi: 10.1002/csc2.20163
   Genomic prediction for resistance to fusarium ear rot and fumonisin contamination in maize

Authors developed genomic selection models to predict maize resistance to Fusarium verticillioides and fumosin contamination. Single-stage univariate and multivariate models were calibrated using different approaches. Fusarium resistance and fumosin content were positively correlated with each other. Prediction accuracy was higher for fumosin content (0.67) and 0.46 for fusarium resistance. Interestingly, the authors found no evidence of significant SNP-trait associations from their genome-wide association study indicating a complex genetic inheritance for the resistance. Marcio Resende, 2020

6/2020 Damon Lisch
Wang, D, et al. 2020. Genetics. 0:doi: 10.1534/genetics.120.303264
   Small RNA-mediated de novo silencing of Ac/Ds transposons is initiated by alternative transposition in maize

Transposable Elements (TEs) are often silenced by their hosts, but how TEs are initially recognized for silencing remains unclear. Here we describe two independent loci that induce de novo heritable silencing of maize Ac/Ds transposons. Plants containing these loci produce dsRNA and Ac-homologous small interfering RNAs (siRNAs), and exhibit decreased levels of Ac transcript and heritable repression of Ac/Ds transposition. We show that these loci comprise inverted duplications of TE sequences generated by alternative transposition coupled with DNA re-replication. This study documents the first case of transposon silencing induced by alternative transposition and may represent a general initiating mechanism for TE silencing.

Most of plant genomes are composed of transposable elements (TEs), and most of them, most of the time, are epigenetically silenced. Because of this, we know a great deal about how silenced transposons are kept silenced. However, it is clear from comparative genomics that over evolutionary or even ecological time scales TEs can be both active and mutagenic. Yet very little is known about how active TEs are recognized, silenced and kept that way. To understand this, it is necessary to observed the killing of naturally active TEs in real time under controlled conditions. Prior to this publication, there was only one example of a locus that could heritably silencing an otherwise active element. With this publication, Wang et al. provide two additional examples. These elements, "Ac-killers", are rearranged Ac elements that express hairpin RNAs that are processed into 21-22nt small RNAs that can heritably silenced active Ac elements. This process is remarkably similar to that observed for Mu killer (Muk), which does the same for MuDR elements. Unlike Muk, however, the precise molecular events that transformed an otherwise active Ac into two Ac killers is described in meticulous detail (there is even a movie). I suspect that Barbara McClintock, who discovered Ac transposition back in the 1940s and who spent years puzzling over the enigma of epigenetic silencing would be pleased by the symmetry of the results provided by Wang et al., which shows how the one can lead neatly and logically to the other. Class II elements like Mu and Ac are prone to rearrangements, and it would appear that the maize genome simply waits for these elements to make a rearrangement that produces an appropriate "antigen", which betrays their presence and leads to their demise. The elegance of this strategy (from the point of view of the host), is that this is just a matter of time and copy number. Eventually, some TE is going to mess up and trigger a host response. With that in mind, it is worth considering the vast number of hairpin transcripts produced by the maize genome, many of which are the source of 21-22 nt small RNAs. It may be that the maize genome (and all plant genomes) are littered with TE killers whose function (loosely defined) is to guard the genome against reanimated TEs. Damon Lisch, 2020

6/2020 Fang Bai
Ou, S, et al. 2020. Nature communications. 11:2288
   Effect of sequence depth and length in long-read assembly of the maize inbred NC358

Significant progress has been made in sequencing technology and assembly methods in different species during the past twenty years. Maize has a large complex genome comprising with repetitive regions and abundant transposable elements. How to improve the read length and depth is the key to assemble the genomes of maize and other crops with broad economic impacts. Ou et al. (2020) sequenced eight assemblies of maize inbred line NC358 genome from 20 to 75X genomic depth and with N50 sub-read lengths of 11-21 kb using the PacBio Sequel platform. They evaluated the completeness and the contiguity of gene-rich regions, transposon-rich regions and the non-TE tandem repeat spaces in each of the assemblies. The authors explored the way to improve the rapid generation of reference-quality assemblies for complex genomes. Fang Bai, 2020

5/2020 Mohammad Arif Ashraf
Zhang, M, et al. 2019. Nature Plants. 5:1297-1308
   A HAK family Na+ transporter confers natural variation of salt tolerance in maize

Higher shoot Na+ content demonstrates reduced biomass of the plant during salt stress. Additionally, it has been known that maize natural variants have a wide range of Na+ exclusion capacity, which indicates that measuring Na+ content in the shoot of inbred lines is an excellent way to find salt tolerant genes in maize. Zhang et al. tested 513 maize inbred lines based on the mentioned hypothesis and from their GWAs study, they have identified the gene and named as Zea mays L. Na+ Content 2 (ZmNC2). Further, they have found that it encodes one of the high-affinity K+ (HAK) transporters, which was previously names as ZmHAK4. CRISPR-generated mutants have demonstrated that ZmHAK4 helps to maintain ion (Na+ and K+) homeostasis. Authors used ZmHAK4-GFP line and expressed in maize protoplasts and tobacco leaf to demonstrate that it is localized in the plasma membrane. Heterologous expression of the transporter provided the idea that ZmHAK4 has Na+-specific transport activity. In a broader picture, ortholog of ZmHAK4 is present in other crop plants with a similar function, which indicates an evolutionary conserved mechanism presented in this manuscript. Mohammad Arif Ashraf, 2020

5/2020 Damon Lisch
Liang, ZK; Qiu, YM; Schnable, JC. 2020. Molecular Plant. 0:doi: 10.1016/j.molp.2020.03.003
   Genome-phenome wide association in maize and Arabidopsis identifies a common molecular and evolutionary signature.

Liang and colleagues have done a masterful job of carefully connecting the dots between loci of known function based on mutant phenotypes using GPWAS (genome-phenome wide association study). The power of this approach is that it captures the contributions of loci that are missed using more traditional approaches, many of which have known mutant phenotypes. By looking at associations of loci with multiple traits, "old friends" with known mutant phenotypes that have not been identified by GWAS, emerge as potential players. Genes identified by GPWAS were more likely to be conserved at syntenic locations, were subject to stronger purifying selection, were expressed at a higher level, and were less likely to be presence absence variants than those identified by GWAS. That is to say, they are more likely to be functional genes, rather than TE-transduplicated "genes" that often complicate analysis of the functional components of complex genomes such as that of maize. Similar results were obtained in Arabidopsis, suggesting that this approach will be useful in a wide variety of plants. Damon Lisch, 2020

5/2020 Fang Bai
Zhang, J et al. 2020. Plant Cell 32:1323-1336
   The cohesin complex subunit ZmSMC participates in meiotic centromere pairing in maize

Both cohesin complex and centromere interaction are important for homologous chromosome pairing during early meiotic prophase I. However the relations between them during chromosome pairing are obscure. Zhang et al. (2020) found a cohesin complex subunit SMC3 indirectly interacts with centromeric histone H3 (CENH3) through chromatin immunoprecipitation (ChIP) mass spectrometry analysis and yeast two-hybrid (Y2H) in maize. The authors showed the enrichment expression of SMC3 on the centromere during the early meiotic stage. In addition, the missing detection of SMC3 on centromere in a cohesion subunit REC8 null mutant in maize suggest that SMC participated in centromere pairing and the cohesion subunit is required for SMC3 assembly. The authors continue to generate the smc3 CRISPR/Cas9 lines and RNAi lines and found the defective centromere pairing during early meiotic prophase I and abnormal chromosome morphology. Zhang et al. uncovered a novel role for SMC3 in centromere pairing and the linkage between the cohesin complex and centromere interaction during the early meiosis stage. Fang Bai, 2020

5/2020 Marcio Resende
Samantha Snodgrass
Wang, BB, et al. 2020. Nature Genetics. 0:doi: 10.1038/s41588-020-0616-3
   Genome-wide selection and genetic improvement during modern maize breeding

The authors sequenced the genome (WGS) of 350 elite inbred lines and investigated the impact of selection during modern maize breeding in China and in the U.S. The lines included public inbred lines and ex-PVP commercial lines in the US, as well as early stage, mid-stage and modern Chinese elite lines. Genome wide association analysis and selection scan methods were combined to identify candidate genes associated with modern breeding. Authors found evidence of convergent increases in allele frequency at putatively favorable alleles for 41.7% of loci for EP, 66.2% for lower leaf angle (LAL), 64.1% for upper leaf angle (LAU) and 49.5% for tassel branch number (TBN) in both the United States and China populations. In addition, evidence of genome-wide parallel selection between China and the United States. The approach was validated in one of the candidate genes using CRISPR-Cas9 knockout lines, which conferred reduced ear height and plant height. Marcio Resende, 2020

Wang and colleagues created a vast phenotypic and genetic resource to identify high-confidence genetic candidates for adaptive, agronomic traits. Their 350 maize lines span the past 60 years of maize breeding in China and the United States, and demonstrate parallel selection for reduced upper leaf angle, tassel branch number, and ASI which are important for high density planting. Population structure and linkage disequilibrium increased while genetic diversity decreased over time. Selective sweeps differed between breeding eras and identified a number of candidate regions, many aligning with previous QTL studies. Two candidates were further validated using CRISPR-Cas9 mutants (ZmPIF3.3 affecting ear height and TSH4 affecting tassel branch number), demonstrating the utility of this resource for linking candidates to traits. Samantha Snodgrass, 2020

5/2020 Samantha Snodgrass
Warman, C, et al. 2020. PLoS Genetics. 0:doi: 10.1371/journal.pgen.1008462
   High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements

In flowering plants, pollen is essential for delivering sperm cells to the egg and central cell for double fertilization, initiating the process of seed development. In plants with abundant pollen like maize, sperm cell delivery can be highly competitive. In an added layer of complexity, growing evidence indicates expression of transposable elements (TEs) is more dynamic in pollen than in other plant tissues. How these elements impact pollen function and gene regulation is not well understood. We used transcriptional profiling to generate a framework for detailed analysis of TE expression, as well as for quantitative assessment of gene function during maize pollen development. TEs are expressed early and persist, many showing coordinated activation with highly-expressed neighboring genes in the pollen vegetative cell and sperm cells. Measuring fitness costs for a set of over 50 mutations indicates a correlation between elevated transcript level and gene function in the vegetative cell. We also establish a role in fertilization for the maize gamete expressed2 (Zm gex2) gene, identified based on its specific expression in sperm cells. These results highlight maize pollen as a powerful model for investigating the developmental interplay of TEs and genes, as well as for measuring fitness contributions of specific genes.

Warman and colleagues sought to understand how high TE activity interacts with the complex developmental and functional processes of male gametophyte cells. They created RNA-seq datasets for tassel primordia, microspores, mature pollen, and isolated sperm cells, combined with published RNA-seq datasets for differential expression analysis and measuring TE activity. They also screened 50+ insertional mutations within highly expressed, candidate genes for male-specific fitness effects. In contrast to Arabidopsis, TE activation occurred earlier in male gametophyte development and remained active through later stages. Most of the insertional mutations had mild male-specific effects on fitness-- the exception being 2 insertional mutations within the gene ZmGEX2 which had severe male-specific effects on fitness. They also found highly expressed pollen stage genes tended to be adjacent to pollen active TEs, though the relationship between these observations remains for further study. Samantha Snodgrass, 2020

4/2020 Fang Bai
Liu, HJ, et al. 2020. Plant Cell. 0:doi: 10.1105/tpc.19.00934
   High-throughput CRISPR/Cas9 mutagenesis streamlines trait gene identification in maize

Applying an improved high-throughput gene editing pipeline to functionally mapped candidates promises high-efficiency gene discovery by large-scale knowledge-informed mutagenesis.

Genome-wide sequence-indexed mutagenesis library based on the random insertion of various elements, such as Activator/Dissociation (Ac/Ds) or Mutator insertion in the genome have been developed in maize for decades and are widely used in genome functional studies. However, the complexity of maize genome reduced the feasibility of current mutagenesis in maize. The recent high-throughput CRISPR/Cas9 mutagenesis in human, rice and soybean improved the specificity and the efficiency of functional genomics study. Liu et al. (2020) made a mutagenesis library of hundred agronomical important maize genes through high-throughput CRISPR/Cas9 editing with the optimized bioinformatics analysis. Their works provide a platform for gene function study to meet the crop breeding development. Fang Bai, 2020

4/2020 Samantha Snodgrass
Jia, HT, et al. 2020. Nature communications. 11:988
   A serine/threonine protein kinase encoding gene KERNEL NUMBER PER ROW6 regulates maize grain yield

Jia and colleagues cloned and characterized KNR6, which they found significantly increased inflorescence meristem length, ear length, and the kernel number per row with increased expression. In sequencing KNR6 among their NILs and 224 diverse inbred lines, they discovered 2 TE PAVs, a harbinger-like element within the 5'-UTR intron and an LTR element ~5.1 kb upstream of the TSS. Lines with the TE insertions showed hypermethylation in these regions and lower expression, leading to decreased ear length and kernel number per row. In vivo immunoprecipitation assays uncovered 58 KNR6-interacting proteins, one of which was an Arf GTP-ase activating protein (AGAP). When this AGAP is mutated, plants also show shorter ear lengths and reduced kernel number per row. Altogether, they propose that the TE insertions inhibit KNR6 expression, and that KNR6 could phosphorylate AGAP leading to increase inflorescence meristem length, ear length, and kernel number per row. Samantha Snodgrass, 2020

4/2020 Marcio Resende
Zhou, P, et al. 2020. Plant Cell. 0:doi: 10.1105/tpc.20.00080
   Meta gene regulatory networks in maize highlight functionally relevant regulatory interactions

The authors analyze a large number of publicly available RNA-seq datasets in maize to create gene regulatory networks of different tissues and genotypes. In total, over 6000 RNA-Seq samples were analyzed to generate 45 co-expression-based GRNs. The authors utilized different methods to construct GRN and observed the best performance when random forest was used. Networks were evaluated by comparing them with publicly available ChIP-Seq data as well as comparing the enrichment of specific Gene Ontologies/metabolic pathways associated with a common transcription factor. The results were also compared with previously published eQTL results to support 68 TFs underlying 74 previously identified trans-eQTL hotspots spanning a variety of metabolic pathways. All the network predictions were made available and represent a new resource for the study of the interaction between transcription factors and targets. Marcio Resende, 2020.

2/2020 Samantha Snodgrass
Rojas-Barrera, IC, et al. 2019. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1817664116
   Contemporary evolution of maize landraces and their wild relatives influenced by gene flow with modern maize varieties

Crop diversity may be essential for adaptation to diverse future climates, and its conservation depends on human practices and preferences. Besides these, we show here that regulations promoting the adoption of modern cultivars can promote rapid changes in the genetic pools of indigenous landraces (LRs) and crop wild relatives (WRs). We compared a wide range of temporal samples of maize LRs and WRs. Modern varieties (MVs), LRs, and their WRs have been in sympatry for over 60 y. We provide genomic evidence of ongoing evolution of Zea mays L. due to introgression from MVs. These findings should foster monitoring strategies and policies that use and safeguard the genetic diversity of maize and its WRs at their center of origin.

Rojas-Barrera and colleagues analyze the genetic similarity of three eras of Mexican landraces and maize wild relatives to Mexican modern maize varieties. As modern varieties increased in usage during the 1990s, there were simultaneous increases in the genetic diversity of landraces, wild relatives, and decreases in Fst between modern varieties and landraces, wild relatives. The strength of these changes was correlated with altitude, where at higher elevations, modern varieties have not been adopted as widely and there is potentially stronger selection for locally adaptive alleles over generalist alleles. Altogether, this indicates gene flow from modern varieties has been constant and pervasive into landrace and wild relative populations and has increased with more widespread adoption. Samantha Snodgrass, 2020

2/2020 Samuel Leiboff
Mejia-Guerra, MK; Buckler, E. 2019. BMC Plant Biology. 0:doi; 10.1186/s12870-019-1693-2
   A k-mer grammar analysis to uncover maize regulatory architecture

As the scale and availability of genomic data increases, data science techniques will play an ever more important role in maize genetics. It is tempting to imagine machine learning as a mysterious black box that will accept raw data and spit out scientific inferences. However, the reality is that data science takes skillful planning and design to make reliable predictions. Mejia-Guerra and Buckler present a machine learning approach to model and detect regulatory sequences that thoughtfully adapts natural language processing models to understand the occurrence and co-occurrence of regulatory motifs throughout the maize genome. They modified the bag-of-words and words2vec model architectures into 'bag-of-k-mers' and 'vector-k-mers' models that process the genome in a series of k-mers. They used data from prior studies of MNase-sensitive open chromatin, Knotted1- and fasciated ear4-bound genomic regions, and TSS-sequencing datasets to train a set of models that is more effective at predicting regulatory activity in B73 than the commonly used MEME tool (which uses empirically-validated sequence motif position weight matrices). They also show that their tool has promise for annotating regulatory sequences in understudied varieties / species by making predictions on the sequenced genomes of maize inbred W22 or closely related grasses, sorghum and rice. What I really love about this paper is the analogy that the authors make between genetic regulatory logic and written sentences, and how they use models for written sentences to understand gene regulation. There are many complex machine learning architectures that the authors could have used to predict regulatory information, however, by constraining their approaches to methods that are ideal for understanding sentences, they were able to design lightweight and interpretable machine learning models. How many other data science solutions are waiting to be transferred to maize genetics? Sam Leiboff, 2020

2/2020 Marcio Resende
Azodi, CB; Pardo, J; VanBuren, R; de los Campos, G; Shiu, SH. 2019. Plant Cell. 0:doi: 10.1105/tpc.19.00332
   Transcriptome-based prediction of complex traits in maize

The motivation of this study was to evaluate if and how can transcriptome information can aid in the phenotypic prediction of complex maize traits. The authors used transcriptome data derived from maize whole seedlings to predict phenotypes (flowering time, height, and grain yield) at much later developmental stages. The prediction accuracies were compared when the models were calibrated using DNA marker data, transcriptome data or a combination of both. In addition, 4 prediction models were tested (rrBLUP, Bayesian Lasso, Random Forest and an Ensemble approach). Results indicated that the Ensemble predictions consistently returned higher predictive abilities compared to the other 3 models tested. Furthermore, the models using transcriptome data underperformed when predicting the complex phenotypes. Combining the transcriptome data to the genomic information also did not improve the predictive ability. Nonetheless, the transcriptome-based models performed well above the baseline model that only captured population structure. Interestingly, transcripts and genetic markers from different genomic regions were identified as important for model predictions and transcript-based models identified more known flowering time-associated genes than genetic marker-based models. While the prediction results did not surpassed the genomic selection models, it was surprising to observe that transcript data generated using V1 seedling tissues can predict adult plant phenotypes, potentially by capturing relationships among genotypes. Marcio Resende, 2020

All data and code needed to reproduce the results from this study are available on GitHub ( DLF1 (GRMZM2G067921), ID1 (GRMZM2G011357), MADS1 (GRMZM2G171365), PEBP8 (GRMZM2G179264), RAP2 (GRMZM2G700665), CCT1 (GRMZM2G381691), CCT2 (GRMZM2G004483), MADS69 (GRMZM2G171650), PEBP2 (GRMZM2G156079), PEBP24 (GRMZM2G440005), PEBP4 (GRMZM2G075081), PEBP5 (AC217051.3_FG006), ZAG6 (GRMZM2G026223), and unknown (GRMZM2G106903).

2/2020 Fang Bai
Zhang, X, et al. 2019. Nature communications. 10:5608
   The tin1 gene retains the function of promoting tillering in maize

The modern domesticated corn has a main stalk and much less tillers than its ancient wild progenitor teosinte, which has multiple tillers. teosinte branched1 (tb1) encodes a TCP transcription factor which is the key gene involved in the maize domestication and repressed the tillers growth. To explore why the modern sweet corn and popcorn still keep growing two or three tillers during the development, Zhang et al. (2019) did a series experiments. They found a QTL locus tiller number 1 (tin1) by constructing a recombinant inbred line (RIL) population of a sweet corn P51 and B73. Tin1 encodes a C2H2-zinc-finger transcription factor and regulates the tiller growth independently to the tb1. Zhang et al. (2019) found that a splice-site variant from G/GT in B73 to C/GT in sweet corn P51 caused the intron retention which enhanced tin1 transcript levels and consequently increased tiller number. Comparative genomics analysis and DNA diversity analysis further revealed that tin1 was under parallel selection in cereals with the 5' splice-site variant were highly correlated with tiller number and this alternative splicing was tissue specific. RNAseq analysis from developing tiller buds identified hundreds DEGs related to photosynthesis and hormone response. The comparative mapping across maize, rice, foxtail millet, and sorghum identified eight copies of tin1 (prog1) in rice, five copies in cultivated foxtail millet and six copies in cultivated sorghum, respectively. Zhang et al. (2019) results provided the evidence that the selection of tin1 across different cereals might share similar genetic basis during modern domestication. Fang Bai 2020.

2/2020 Mohammad Arif Ashraf
Liu, M, et al. 2020. Plant Biotechnology Journal. 18:207-221
   Analysis of the genetic architecture of maize kernel size traits by combined linkage and association mapping

Kernel size, which includes kernel length, width, and thickness, is one of the major traits for high yielding maize varieties. Liu et al. took the advantage of an association panel, which contains 310 maize inbred lines, and grow them in several environmental conditions to identify candidate genes associated with kernel size. Along with the potential SNPs, they have identified 7 miRNAs in the targeted regions and one of them, zma-miR164e targets CUC1, CUC2, and NAC6. Further experiment on Arabidopsis plant showed that overexpression of zma-miR164e downregulates CUC1, CUC2, and NAC6 and results in the failure of seed formation. Interestingly, miR164e targets NAC30, NAC108, and NAC113. This study has highlighted the role of identified zma-miR164e for regulation seed development and yield in both Arabidopsis and maize. Arif Ashraf, 2020

2/2020 Damon Lisch
Doll, NM, et al. 2020. Plant Cell. 0:doi: 10.1105/tpc.19.00756
   Transcriptomics at maize embryo/endosperm interfaces identifies a transcriptionally distinct endosperm sub-domain adjacent to the embryo scutellum

It is not every day that you discover a new, distinct and important cell layer, but that is what this group has done. The freshly named endosperm adjacent to scutellum (EAS) appears only briefly during maize kernel development and is not structurally distinct but appears to be important for communication between the embryo and the endosperm. Perhaps not surprisingly, its distinct transcriptome is enriched for, you guessed it, transporters. And a mutant that eliminates the embryo dramatically changes expression of genes in the EAS. This is a very nice example of discovery-based science, where what is most important is not the quantity of the data produced, but the choice of where and when to look for the data. Extra credit for providing a very nice visualization tool: Extra extra credit for supplying an exceptionally detailed Materials and Methods section. Damon Lisch, 2020

Data from this paper is avaible at MaizeGDB- on the gene pages.

1/2020 Samantha Snodgrass
Ricci, WA, et al. 2019. Nature Plants. 0:doi: 10.1038/s41477-019-0547-0
   Widespread long-range cis-regulatory elements in the maize genome

Ricci and colleagues (2019) assayed accessible chromatin regions of maize using ATAC-seq to identify potential cis-regulatory elements. Of the non-genic regions they identified, 35% (10,433 regions) were >2 kb from their nearest gene, indicating potential long-range cis-regulatory elements. Using analysis of sequence diversity, eQTLs, histone modifications, ChIP-seq, chromatin loop interactions (hi-C), and transcriptional enhancer activity (STARR-seq), these distal accessible chromatin regions appear to be functional, associated with gene expression and phenotypes, and acting in cis with their target loci. Taken together, long-range cis-regulatory elements are present and common within the maize genome and may have substantial impacts on gene expression and phenotype.

1/2020 Samuel Leiboff
Knauer, S, et al. 2019. Genome Res. 0:doi: 10.1101/gr.250878.119
   A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits

The shoot apical meristem (SAM) contains a body of pluripotent stem cells that produce leaves, axillary buds, veins, internodes, and all of the cell types that make up the mature plant. So if we want to precisely control plant architecture, we should start with understanding how the SAM is organized and maintained. Although all plants that produce leaves or flowers during the growing season maintain SAMs, the exact anatomy of the SAM can be different between evolutionary groups. Maize (representative of other grasses) makes a domed SAM with 2 distinct layers but Arabidopsis (representative of many other eudicots) makes a flat vegetative SAM with 3 distinct layers. And while genetic mutants and molecular analysis have determined that the Arabidopsis SAM is comprised of a central zone (CZ) of stem cells, an organizing center (OC) that maintains stem cells, and a peripheral zone (PZ) where leaves or other lateral organs are formed, the maize SAM only seems to share a few similarities on a gene-by-gene basis. To address the differences between maize and Arabidopsis meristem organization, they compared the maize homologues of Arabidopsis SAM domain genes and found largely divergent domain expression patterns between species. When Knauer et al. used known and predicted transcription factor (TF) expression values to try and tease apart the regulatory network of gene families within the maize SAM, they detected a strong hierarchy of both activating and repressing TF activity upstream of putative CZ genes. Together, they use this data to suggest that the functional organization of the maize SAM differs dramatically from Arabidopsis. In the absence of detectable ZmWUS1 or other WOX expression in the L2 meristem core, they hypothesize that L1-expressed ZmWOX9b and ZmWOX9c may take the place of the stem-cell maintenance signal found in the Arabidopsis OC. Whereas Arabidopsis WUS1 moves upward to the L1 layer of the SAM and drives repressive CLE signaling that leads to stem cell homeostasis, they propose an analogous downward signal from ZmWOX9b and ZmWOX9c that is met with repressive FEA2/ZmFCP1 signaling that stabilizes the stem cell population in maize. In other words, stem cell regulation in the maize SAM is balanced, but inside-out or upside-down compared to Arabidopsis! Sam Leiboff, 2020

All raw and processed sequencing data generated in this study have been submitted to the NCBI Gene Expression Omnibus (GEO; under accession number GSE137715 and to the NCBI Sequence Read Archive (SRA; under accession number SRP101301.

All raw and processed sequencing data generated in this study have been submitted to the NCBI Gene Expression Omnibus (GEO; under accession number GSE137715 and to the NCBI Sequence Read Archive (SRA; under accession number SRP101301.

1/2020 Mohammad Arif Ashraf
Liang, L, et al. 2019. Plant Physiol. 0:doi: 10.1104/pp.19.00894
   A sequence-indexed Mutator insertional library for maize functional genomics study

ChinaMu project database is available at:

It has been a decade since we have maize reference genome sequenced. Unfortunately, in this time period, the number of sequence-indexed insertional libraries did not grow as rapidly compared to other model plants such as Arabidopsis and rice. For instance, 74% Arabidopsis genes are covered by 88,000 T-DNA insertion lines and 60% rice genes are targeted by 2,46,566 T-DNA, Ds/dSpm, or Tos17 insertions. On the other hand, among 44,300 annotated maize genes, UniformMu covers only 15,950 genes in 39,864 insertion lines. Liang et al. generated a Mu insertional library, ChinaMu. In this process, they have crossed a Mu-starter line contained MuDr and a1-mum2 gene as paternal line to B73 as maternal line. They have successfully isolated 66,565 insertion lines which cover 45.7% annotated maize genes. Combining UniformMu with ChinaMu, now 52.2% annotated maize genes are tagged by sequence-indexed insertional libraries. The recent addition of ChinaMu resource in the maize community will accelerate the functional study of maize genes.

1/2020 Marcio Resende
Liu, JN et al. 2020. Genome Biol 21:121
   Gapless assembly of maize chromosomes using long read technologies

The authors report the sequencing and assembly of B73 containing a meiotic drive system on Abnormal chromosome 10 (B73-Ab10). Ab10 is longer than chromosome 10 and contains long spans of uncharacterized DNA including a cluster of Kinesin driver (Kindr) genes required for meiotic drive. The authors combined long-read sequencing technologies Nanopore and Pacbio with the BioNano Saphyr optical mapping system. Merging the two independent assemblies (PacBio and Nanopore) significantly improved assembly quality and resulted in a final assembly that includes gapless telomere-to-telomere assemblies of two chromosomes (3 and 9). The work reports the first full assembly of a meiotic drive haplotype, which was found to contain three fully assembled TR-1 knobs, a much larger knob180 knob, and two large inversions (4.4 and 8.3 Mb) that are homologous to normal chromosome 10. These major structural differences help to explain why recombination between the Ab10 haplotype and normal chromosome 10 is suppressed.

1/2020 Fang Bai
Wu, QY, et al. 2019. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1917577116
   The maize heterotrimeric G protein β subunit controls shoot meristem development and immune responses

Cereal crops, such as maize, provide our major sources of food and feed. Crop productivity has been significantly improved by the selection of favorable architecture and development alleles; however, crops are constantly under attack from pathogens, which severely limits yield due to a defense-growth trade-off. Therefore, identifying key signaling regulators that control both developmental and immune signaling is critical to provide basic knowledge to maximize productivity. This work shows that the maize G protein β subunit regulates both meristem development and immune signaling and suggests that manipulation of this gene has the potential to optimize the trade-off between yield and disease resistance to improve crop yields.

Guanine nucleotide-binding proteins (G proteins) are reported to transmit signals in both animal and plants. Heterotrimeric subunit interacts with the CLAVATA receptor to control the shoot apical meristem size and growth in maize and Arabidopsis. null alleles in Arabidopsis are viable, but are seedling lethal in maize. In this paper, Wu et al. (2020) made a CRISPR/Cas9-induced null alleles of (Zmgb1CR) and found that the early lethal seedling phenotypes in maize are due to the auto-immune responses. They detect the higher level of defense hormone salicylic acid and the expression of the immune marker genes, PATHOGENESIS-RELATED PROTEIN1 (PR1) and PR5 expression in Zmgb1CR mutants compared to the wild type controls. Wu et al. also found a suppressive genetic background CML103 by crossing viable heterozygotes of Zmgb1CR into 25 NAM lines. They identified a fascinated ear EMS mutant line which encodes a viable Zmgb1 mutant allele. By doing a series of genetic cross and yeast 3-hybrid (Y3H) experiments, the authors found that ZmGB1 interact with CT2/Gα and FEA2 CLAVATA receptor to regulate inflorescence development and kernel row number, as well as the plant immunity. Their work indicates the G protein roles in crop yield and disease defense.

12/2019 Carolyn Rasmussen
Zhang, ZH, et al. 2019. Plant Cell. 0:doi: 10.1105/tpc.19.00486
   A large transposon insertion in the stiff1 promoter increases stalk strength in maize

Lodging can reduce yield. Maize inbreds using for generating hybrids fall into stiff-stalk and non-stiff-stalk groups. The stiff1 gene (Zm00001d036653), encoding an F-box protein, is disrupted by a transposable element in about half of the stiff-stalk lines, thereby increasing lignin and cellulose accumulation. Gene editing using CRISPR-Cas9 to mutate stiff1 also increased stalk strength, which lead to increased expression of NAC-MYB transcription factors important for secondary cell wall biosynthesis. Identification of this gene may lead to increased ability to use marker assisted breeding to select for stalk stiffness. Carolyn Rasmussen 2019

12/2019 Sarah Hake
Wu, JR et al. 2019. Proc Natl Acad Sci, USA pp.doi; 10.1073/pnas.1902593116
   Overexpression of zmm28 increases maize grain yield in the field

In the approaching decades, food security will likely be more of an issue as there will be an increased demand for grain which will need to be met in an environmentally sustainable manner. To date, commercial transgenic maize has primarily targeted resistance to insects and herbicides. Here we describe a transgenic approach to improve the yield and yield stability of maize. We have demonstrated that increasing and extending the expression of a maize gene, zmm28, alters vegetative and reproductive growth parameters and significantly enhances yield in large-scale field trials conducted over multiple years. We conclude that alteration in expression of a native maize gene in maize can create a substantially positive change in a complex trait like grain yield.

12/2019 Damon Lisch
Dong, ZB et al. 2018. Nucl Acid Res 46:5012-5028
   Transcriptional and epigenetic adaptation of maize chromosomes in Oat-Maize addition lines

This is one of those studies in which previous and important research done by geneticists is revisited using modern techniques. It explores the way in which two distinct genomes can interact within shared nuclei. Oat and maize are far enough from each other that this particular kind of polyploid is unlikely to have occurred naturally. However, the vast differences between these two genomes, along with the fact that only a subset of maize chromosomes are retained, make this a fascinating tool for understanding cis and trans regulation of "alien maize genes" (love that phrase) in an oat nuclear environment. The results suggest that a majority of maize genes do not change their expression and that those that do are more likely to be syntenic genes, suggesting that these more highly conserved genes are more connected to the rest of the genome. They also found evidence that changes in centromeres in the maize addition centromeres were associated with changes in gene expression, and that chromatin changes largely mirrored changes in gene expression. Changes in transposon activity in histone modifications were not reported, which represents a missed opportunity, but the data is certainly available for re-analysis and the results of that analysis would be interesting. Damon Lisch, 2019

12/2019 Sarah Hake
Wang, J et al. 2019. New Phytol pp.doi: 10.1111/nph.15890
   krn1, a major quantitative trait locus for kernel row number in maize

In this manuscript the group fine-mapped a QTL called kernel row number 1 to a 6.6kb region in close proximity to an AP2 gene first identified as indeterminate spikelet1 and also as Tasselseed6 (Chuck et al., 1998; Chuck et al., 2007). Ts6 was identified as a dominant mutation that harbors a mutation in the binding site of Mir172. ids1 is a loss of function allele. The ortholog in wheat is the Q gene, important in wheat domestication. Wang et al provide confidence that indeed IDS1 is KRN1 by performing an association mapping with 245 lines and seeing strong signal in the promoter of IDS1, where KRN1 was fine-mapped. They analyzed two mutants containing nucleotide changes in the microRNA binding site. The mutants had more kernel rows albeit smaller ears. It is nice to see new functions assigned to old friends. Sarah Hake, 2019 Chuck, G., Meeley, R., Hake, S., 1998. The control of maize spikelet meristem fate by the APETALA2-like gene indeterminate spikelet1. Genes and Development 12, 1145-1154. Chuck, G., Meeley, R., Irish, E., Sakai, H., Hake, S., 2007. The maize tasselseed4 microRNA controls sex determination and meristem cell fate by targeting Tasselseed6/indeterminate spikelet1. Nat Genet. 12, 1517-1521.

12/2019 MaizeGDB Staff
Feng, C et al. 2019. Plant J pp.DOI: 10.1111/tpj.14606
   The deposition of CENH3 in maize is stringently regulated

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12/2019 Fang Bai
Zheng, XX, et al. 2019. Plant Cell. 0:doi: 10.1105/tpc.19.00444
   Intra-kernel reallocation of proteins in maize depends on VP1-mediated scutellum development and nutrient assimilation

During the double fertilization in angiosperms, the pollen tube delivers two sperm to the embryo sac then one haploid sperm fuses with the haploid egg to form the diploid embryo, and the other one fuses with the diploid central cells to form the triploid endosperm. Endosperm in maize is a persistent organ to store the nutrient and nourish the embryo development. How does the embryo communicate with the endosperm during the seed development? In this article, Zheng et al. (2019) found the reduced level of zein proteins and the increased levels of non-zein proteins in different zein mutants by SDS-PAGE analysis. The further mass spectrometric analysis, immunoblotting analysis and in situ hybridization showed that the upregulated of the Globulin1 (GLB1) and GLB2 in those zein mutants accompanied by the enlarged cell size in the scutellum. Transcriptome experiment and GO analysis in the zien mutant embryo at two developing stages showed a significant number of genes responding to nutrient rebalancing and carbohydrate metabolism pathway. The authors also did a series of experiments to show that the ABA regulated gene VP1 is required for protein reallocation from the endosperm to embryo through trans-activating Glbs and other genes in ABA pathway. Fang Bai, 2019���

11/2019 Sarah Hake
Leiboff, S; Hake, S. 2019. Curr Biol. 0:doi: 10.1016/j.cub.2019.08.044
   Reconstructing the transcriptional ontogeny of maize and sorghum supports an inverse hourglass model of inflorescence development

Leiboff sequenced individual sorghum panicles and maize tassels at different developmental stages and calculated expression trajectories for each species using a pseudotime metric, nick-named developmental time units. In general, this metric matched inflorescence length and days after sowing. The transcriptional data identified 5 developmental stages in maize and 4 in sorghum that correlated with changes in tissue identity. Many of the maize genes identified by mutant phenotypes were expressed at similar developmental time units in sorghum, such as branched silkless, bearded ear, and ramosa1, but there were some striking exceptions such as liguleless1 and ramosa3. Both maize and sorghum have a developmental stage when the genes that are expressed are anciently conserved across all plant taxa. This stage is called the hour-glass. Interesting, the hour-glass stages of maize and sorghum did not line up, suggesting that selective pressures on each species has differed despite their relatively recent evolution. Sarah Hake, 2019

Maize tassel raw RNaseq reads are in NCBI SRA: BioProject: PRJNA551002 Sorghum panicle raw RNaseq reads are in NCBI SRA: BioProject: PRJNA551005

Maize tassel raw RNaseq reads are in NCBI SRA: BioProject: PRJNA551002 Sorghum panicle raw RNaseq reads are in NCBI SRA: BioProject: PRJNA551005

11/2019 Fang Bai
Zhang, X, et al. 2019. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1902747116
   Maize sugary enhancer1 (se1) is a gene affecting endosperm starch metabolism

Maize sugary enhancer1 (se1) is a genetic modifier of su1 expression and is a commercially important allele that modifies kernel carbohydrate metabolism and improves fresh market quality. Carbohydrates, and primarily starch, are a major globally important product of cereal grains, but mechanisms affecting grain composition and genetic networks are not fully understood. In this study, we identify a gene that affects endosperm carbohydrate composition by modifying metabolism in a sugary1 background. This discovery provides another entry point to understand metabolism and genetic background effects in cereal grains.

Starch synthesis, accumulation and metabolites are the major effects on the yield of crops. sugary enhancer1 (se1) is a naturally uncharacterized mutant and a recessive modifier ofsugary1 (su1) which is important for starch biosynthesis. To characterize the se1 mutant kernels, Zhang et al. (2019) developed two near-isogenic lines, W822Gse (su1-ref/su1-ref se1/se1) and W822GSe (su1-ref/su1-ref Se1/Se1) in a su1-ref background. They found that both mature and developing kernels of mutants contained more water soluble polysaccharide and less starch than normal control lines. Map-based cloning identified an unknown function gene Zm00001d007657 which expressed abundantly in the endosperm and embryo. In order to understand the role of Se1 in metabolism, the authors carried out the metabolic analysis to compare the se1 mutants to their normal isogenic lines and B73 inbred line by gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography-MS (UPLC-MS). UPLC-MS analysis showed that the mutants exert little effects on lipid metabolism during seed development. GC-MS and 2-way ANOVA analysis identified 15 metabolites which have significant changes in carbohydrate metabolism in se1mutants. Among them, sucrose and maltose were the only two sugar-related signatures. Transcriptome analysis through RNA-seq at 11, 15, and 19 DAP of endosperm showed that the starch and sucrose metabolic pathway involved in the se1 kernel development. The authors also made the RNAi lines to validate the correct cloning and the function of the Se1 in starch biosynthesis. This work has the significant impacts on our understanding of starch metabolism and improving modern sweet corn breeding. Fang Bai, 2019

11/2019 Damon Lisch
Noshay, JM, et al. 2019. PLoS Genetics. 15:e1008291
   Monitoring the interplay between transposable element families and DNA methylation in maize

Maize, like many other crops, has a complex genome that is primarily composed of transposable elements (TEs). These TEs play major roles in shaping the epigenome and have the potential to influence genes or regulatory regions. Although many studies assess the average patterns of chromatin at all TEs, there is evidence for significant variation among different TE families. We find that TE families have distinct patterns of DNA methylation in flanking regions. These differences can be explained by a combination of preferential insertion of some families into methylated or unmethylated genomic regions as well as the potential for some TE families to trigger methylation of flanking regions. Understanding the interplay of TE families and chromatin can help understand the mechanisms through which TEs influence genes and shape crop genomes.

Much of the maize genome is composed of transposable elements, and most of those elements are methylated and epigenetically silenced. Based on these observations, it is tempting to view TEs and inert, interchangeable and essentially irrelevant parts of the genome. However, recent observation by Noshay et al suggests that the situation is far more complex, and far more interesting, than that. The authors exploit the ubiquitous TE polymorphisms in maize to demonstrate that these polymorphisms are associated with epigenetic polymorphism not just in the elements themselves, but in sequences flanking those elements. Interestingly, the authors find evidence that TE families may target distinct epigenetic domains, consistent with a genome ecology model, in which different TEs occupy distinct niches within genomes. Although there is certainly evidence for effects on expression of genes near TEs, the overall effect of TE insertions with respect to local cis-acting epigenetic modification remains poorly understood. With its vast array of polymorphic insertions, maize is an excellent model for understanding the complex relationship between TEs and their hosts. Damon Lisch, 2019

11/2019 Carolyn Rasmussen
Ren, Z; et al. 2019. Oxf Surv Plant Mol Cell Biol. 0:DOI:
   Cryo-EM Structure of Actin Filaments from Zea mays Pollen

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10/2019 Fang Bai
Dong, ZB, et al. 2019. Nature communications. 10:3810
   The regulatory landscape of a core maize domestication module controlling bud dormancy and growth repression

TEOSINTE BRANCHED1 (TB1) is a transcription factor belongs to the TCP family in plant. TB1 functions in the repression of the axillary branching and the crop domestication. To identify TB1 regulation in crop apical dominance growth, Dong et al. did a series of omics and biochemical experiments on 1mm of B73, tb1 and grassy tillers1(gt1) tiller buds at different developmental stages. They found that several phytohormones such as gibberellins, abscisic acid and jasmonic acid, the sugar level, and some other domestication genes TEOSINTE GLUME ARCHITECTURE1(TGA1) and GT1 integrated with TB1 to regulate the axillary bud dormancy and the plant apical dominance. The efficiency of future agriculture engineering will benefit from their work to increase the crop yield. Fang Bai, 2019

10/2019 Sarah Hake
Hughes, TE et al. 2019. Development pp.doi: 10.1242/dev.177543
   Redundant SCARECROW genes pattern distinct cell layers in roots and leaves of maize

A homeolog, or paralog generated by genome or partial genome duplication, of ZmSCARECROW1 was identified and called ZmSCARECROW1h. Single mutants had minor phenotypes while double Zmscr1 Zmscr1h mutants were small, had reduced midrib length and lacked endodermal cells separating vasculature from cortex cells in the roots. In addition, Zmscr1 Zmscr1h double mutants produced fewer mesophyll cells but often had supernumerary bundle sheath-like cells. The extra bundle sheath-like cells sometimes produced an enzyme required for photosynthesis, suggesting they still had bundle-sheath function. Both ZmSCR1 and ZmSCR1h transcripts accumulated in ground meristem cells located around developing veins. Lack of mesophyll cells in the double mutant then suggests that ZmSCR1 and ZmSCR1h promote divisions that produce mesophyll cells and prevent ectopic divisions in nearby layers. The Zmscr1 Zmscr1h double mutants also produced excess intermediate veins with lignified sclerenchyma. Overall, these data suggest that ZMSCR1 and ZmSCR1h play an important, redundant function in radial patterning in roots and shoots. Carolyn Rasmussen

Hughes and colleagues analyzed the double mutant of the maize scarecrowgenes and found a leaf and root phenotype. As described for Arabidopsis scarecrowmutants, root lacks the endodermis. Leaves are droopy possibly because the midrib does not extend as far. Veins are separated by 1 mesophyll cell instead of 2. Bundle sheath cells were specified correctly, but occasionally there was an ectopic bundle sheath cell. The maize scrgenes are expressed in the ground meristem cells that surround developing veins early in leaf development. Sarah Hake, 2019

10/2019 Carolyn Rasmussen
Wang, HL, et al. 2019. PLoS Genetics. 15:e1008377
   BZU2/ZmMUTE controls symmetrical division of guard mother cell and specifies neighbor cell fate in maize

A mutant, Zmbizui2/Zmmute, was identified by high leaf-surface temperature, pale leaves and a seedling lethal phenotype. The disrupted gene identified was orthologous to the transcription factor MUTE required for stomatal development and first described in Arabidopsis thaliana. The Zmbizui2/Zmmute mutant formed guard mother cells that did not promote subsidiary cell polarization or subsequent development. Instead, guard mother cells divided aberrantly to form several undifferentiated cells, suggesting ZMMUTE may also prevent ectopic guard mother cell divisions. The ZmMUTE protein localized to guard mother cells and subsidiary cells, disappearing from guard mother cells after their symmetric division. When expressed in Arabidopsis, the ZmMUTE protein moved between cells only when it had the C-terminal domain, suggesting that this domain is important for its movement. ZmMUTE bound directly to promoters of genes required for subsidiary cell development, PAN1 and PAN2, potentially with other yet unknown transcription factors, and directly or indirectly regulated expression of other genes required for subsidiary cell development. Carolyn Rasmussen, 2019

10/2019 Damon Lisch
Wang, C, et al. 2017. New Phytol. 0:doi: 10.1111/nph.14688
   A transposon-directed epigenetic change in ZmCCT underlies quantitative resistance to Gibberella stalk rot in maize

This is one of those studies that beautifully weaves together multiple lines of evidence that suggest that a TE insertion upstream of a gene disrupts a delicate balance that keeps that gene epigenetically poised to respond to infection. In the absence of the insertion, the gene, ZmCC2 is not expressed and is regulated by a balance of repressive H3K27me3/H3K9me3 and active H3K4me3 histone marks. On infection, the repressive marks are transiently lost, and the gene expresses, resulting in resistance to the pathogen. When the TE is present, this balance is disrupted, resulting in a reduction of H3K4me3, an increase in spreading of DNA methylation and a reduction of transient expression and disease resistance. These observations suggest that among their many effects, TEs can alter the local chromatin environment and have important effects on nearby gene expression. They also suggest that when looking for causal polymorphisms associated with strong effect QTLs, we should take TEs seriously, particularly given the high frequency of causal polymorphisms that map outside of genes. Damon Lisch, 2019

10/2019 MaizeGDB Staff
Roessler, K, et al. 2019. Nature Plants. 0:doi: 10.1038/s41477-019-0508-7
   The genome-wide dynamics of purging during selfing in maize

Inbreeding depression, or self-fertilization of plants leading to reduced vigour and fertility, is thought to be caused by increased homozygosity, which increases the genetic load by uncovering recessive deleterious alleles and/or eliminating heterozygosity at loci with an overdominant advantage. One way to combat the increased load caused by inbreeding is the removal, or "purging", of recessive deleterious alleles. When purging is effective, there may be no inbreeding depression. Recently, researchers have argued that genomic data provide more precise insights into inbreeding effects than previous approaches. Here, this extends this argument to the phenomenon of purging. In this study, the authors use an experimental evolution approach to investigate the dynamics of purging on a genome-wide scale. The experiment consists of 11 outcrossed maize parental lines that were self-fertilized for six or more generations. Results led to documented rapid genome-size loss in 3 of 11 selfed lineages. These observations add to a growing consensus that genome size can change rapidly in plant species. TEs made up the largest proportion of genome loss. Finally, deleterious single nucleotide polymorphisms were lost more rapidly in regions of high recombination, presumably because recombination increases the efficacy of selection by uncoupling linked variants. Maggie Woodhouse, 2019

10/2019 Sarah Hake
Liu, QJ et al. 2019. Proc Natl Acad Sci, USA 116:19736-19742
   NEEDLE1 encodes a mitochondria localized ATP-dependent metalloprotease required for thermotolerant maize growth

Meristems are highly regulated groups of stem cells that are ultimately responsible for the formation of all branches, lateral organs, and stems in plants, and thus directly affect plant architecture and crop yield. We have identified a highly conserved member of a family of mitochondria-localized proteases that regulates maize inflorescence architecture. Unlike in Arabidopsis, in which its function appears dispensable, we have discovered that this protein is required for maize growth and productivity in field conditions and in high temperatures, and we provide evidence that it maintains reproductive meristem redox status and auxin homeostasis. These data highlight the importance of meristem redox status for sustaining maize organogenesis in challenging environments.

9/2019 Sarah Hake
Tian, JG, et al. 2019. Science. 365:658-664
   Teosinte ligule allele narrows plant architecture and enhances high-density maize yields

Tian et al measured leaf angle in recombinant inbred lines made between teosinte and W22. They found two loci, UPRIGHT PLANT ARCHITECTURE1(UPA1) and UPA2 that quantitatively affected leaf angle. UPA2 is a 2 nucleotide cis-regulatory sequence upstream of the transcription factor, RAVL1. This sequence is not found in any maize lines and is only present in a few teosintes. It is bound by DROOPING LEAF, which interacts with LIGULELESS1. The other QTL, UPL1, is downstream of RAVL1 and encodes the final enzyme in BR biosynthesis. The RAVL1 knockout and the near isogenic maize line carrying the teosinte UPA2 allele have higher yields than control maize lines in field conditions. They also transferred the sequences into elite crop lines, showing an increase in yield at the highest planting densities. Sarah Hake, 2019

9/2019 Fang Bai
Alvarez, CE, et al. 2019. Nature Plants. 0:doi:10.1038/s41477-019-0451-7
   Molecular adaptations of NADP-malic enzyme for its function in C4 photosynthesis in grasses

C4 plants, such as maize, have higher efficiency of photosynthesis than C3 plants by fixing CO2 through an alternative C4 photosynthetic pathway. Both mesophyll and bundle sheath cells in C4 plants are involved in photosynthesis. In mesophyll cells, CO2 is fixed to a four-carbon compound called malate. When malate is transported to the bundle sheath cells, it is mainly decarboxylated by nicotinamide adenine dinucleotide phosphate (NADP)-malic enzyme (C4-NADP-ME) to release CO2 and enter the C3 plant Rubisco-Calvin Cycle. To study the molecular mechanism of the C4-NADP-ME enzyme activity on malate, Alvarez et al. crystallization of the C4-NADP-ME from maize and sorghum, and identified several C4-specific amino acids. The authors introduced those single amino acid mutants to study the evolution of the C4 property, and found that both amino acid E339 and���140 are the critical position for the C4-NADP-ME regulation of photosynthesis. The authors study provides tools for future synthetic biology to improve the efficiency of the photosynthesis and increase the crop yield. Fang Bai, 2019

9/2019 Carolyn Rasmussen
Hughes, TE et al. 2019. Development pp.doi: 10.1242/dev.177543
   Redundant SCARECROW genes pattern distinct cell layers in roots and leaves of maize

A homeolog, or paralog generated by genome or partial genome duplication, of ZmSCARECROW1 was identified and called ZmSCARECROW1h. Single mutants had minor phenotypes while double Zmscr1 Zmscr1h mutants were small, had reduced midrib length and lacked endodermal cells separating vasculature from cortex cells in the roots. In addition, Zmscr1 Zmscr1h double mutants produced fewer mesophyll cells but often had supernumerary bundle sheath-like cells. The extra bundle sheath-like cells sometimes produced an enzyme required for photosynthesis, suggesting they still had bundle-sheath function. Both ZmSCR1 and ZmSCR1h transcripts accumulated in ground meristem cells located around developing veins. Lack of mesophyll cells in the double mutant then suggests that ZmSCR1 and ZmSCR1h promote divisions that produce mesophyll cells and prevent ectopic divisions in nearby layers. The Zmscr1 Zmscr1h double mutants also produced excess intermediate veins with lignified sclerenchyma. Overall, these data suggest that ZMSCR1 and ZmSCR1h play an important, redundant function in radial patterning in roots and shoots. Carolyn Rasmussen

Hughes and colleagues analyzed the double mutant of the maize scarecrowgenes and found a leaf and root phenotype. As described for Arabidopsis scarecrowmutants, root lacks the endodermis. Leaves are droopy possibly because the midrib does not extend as far. Veins are separated by 1 mesophyll cell instead of 2. Bundle sheath cells were specified correctly, but occasionally there was an ectopic bundle sheath cell. The maize scrgenes are expressed in the ground meristem cells that surround developing veins early in leaf development. Sarah Hake, 2019

9/2019 Damon Lisch
Xue, W, et al. 2019. Genetics. 0:doi: 10.1534/genetics.119.302378
   Hybrid decay: A transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize

This is one of those observations that is intriguing enough to invite spirited debate. The phenomenology is fascinating. Essentially, the authors have identified an accession of teosine that, when back crossed to maize, give rise to uniformly sickly plants. Subsequent back crosses again give rise to only sickly plants. Obviously, this means mapping whatever is causing this trait is not possible. Once the sickly phenotype appears in a lineage, normal plants are never again recovered by continued backcrossing to the normal maize parent. Very cool, and quite reminiscent of paramutation. I am actually surprised that this possibility was not raised. Expression and structural variation analysis are not terribly illuminating with respect to mechanism, however, it appears that 22nt small RNAs (which are often trans-acting) may be involved, and the authors speculate that mis-regulation of TEs and associated genes may be causing the sickly phenotype, but certainly no smoking gun here. However, rigorous description of unexpected phenomena, in this case, 'hybrid decay', lies at the heart of novel areas of exploration. Damon Lisch, 2019

8/2019 Sarah Hake
Anderson, AA, et al. 2019. Plant Cell. 0:doi: 10.1105/tpc.18.00840
   The second site modifier, Sympathy for the ligule, encodes a homolog of Arabidopsis ENHANCED DISEASE RESISTANCE4 and rescues the liguleless narrow maize mutant

The phenotype of Liguleless narrow (Lgn-R) mutants is dependent on inbred background. In this paper, the main effect modifier, sympathy for the ligule (sol) was cloned and shown to encode a homolog of ENHANCED DISEASE RESISTANCE4 from Arabidopsis. Plants with the rescuing haplotype of sol are nearly normal and survive hot temperatures. Plants with the severe haplotype are short, missing ligules, and die at hot temperatures. A phosphoproteome and RNAseq suggests that Lgn-R mutants display signs of PAMP triggered autoimmunity. Sarah Hake, 2019

8/2019 Fang Bai
Zhang, JY, et al. 2019. J Cell Biol. 0:doi: 10.1083/jcb.201807166.
   Maize defective kernel5 is a bacterial TamB homologue required for chloroplast envelope biogenesis

The plant chloroplast is an important organelle which involves in the photosynthesis and starch biosynthesis. Zhang et al. identified series alleles of a maize defective kernel5 (dek5) with a range of severity. The reference dek5 mutant endosperm has a fewer but larger size of starch granule, as well as the reduced zein content than in normal endosperm. This phenotype was also found in the rice homologue ssg4 mutant. The authors observed the elevated of the ADP-glucose and sucrose in dek5 which indicated that DEK5 might involve in the starch biosynthesis. The defective of the chloroplast revealed by TEM and GFP labeling experiments affected the protein transportation and resulted in the pale green leaf or the lethal seedlings. Through the map-based cloning Zhang et al. found that DEK5 encoded a bacterial TamB homologue which is critical for membrane biogenesis. The further series of the biochemical experiments on chloroplast fractions of the envelope membrane and the thylakoid membrane showed that the DEK5 is specific localized on the chloroplast envelope. Zhang et al. carried out a dual-protease protection assay for the DEK5 topology using the thermolysin and the trypsin, and found that DEK5 protein located between the OEM and IEM which is similar to the TamB in E. coli and TIC236 in Arabidopsis, but different from the SSG4 in rice. Proteomics analysis on the chloroplast envelope fraction and Pi uptake assay on purified chloroplast showed that DEK5 roles in envelope protein accumulation and metabolite transport. Fang Bai, 2019

7/2019 Carolyn Rasmussen
Gumber, HK, et al. 2019. Nucleus. 10:144-166
   MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation

This study identifies the first outer nuclear membrane protein in plants as required for successful clustering of telomeres on the nuclear envelope during mid prophase. It is crucial for proper chromosome segregation during meiosis and pollen viability. It is also the first KASH protein to be placed in the stomatal development pathway, reflecting the pleotropic nature of this highly conserved gene. Hardeep Gumber, 2019

7/2019 MaizeGDB Staff
Hake, S. 2019. Plant Cell. 31:1202-1203
   Identification of cup-shaped cotyledon: New Ways to Think about Organ Initiation

This inspiring editorial outlines the importance and usefulness of old-fashion detailed analysis of aa Arabidopsis mutant, cuc, and how that work brings significantly more meaning to later genomic era analysis. A shout out to the awesome power of genetics! MaizeGDB Staff, 2019

7/2019 Fang Bai
Zhang, ZY; Dong, JQ; Ji, C; Wu, YR; Messing, J. 2019. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1904995116
   NAC-type transcription factors regulate accumulation of starch and protein in maize seeds

Starch and protein are two main compounds in maize endosperm which decide the yield of the corn products. Zhang et al. identified two NAC transcription factors ZmNAC128 (previously named nrp1) and ZmNAC130 (previously named nactf130) that regulate the starch and protein accumulation in maize. Both NAC genes are specific expressed in the starch endosperm cells. Knock-down mutants of nacRNAi showed the significant reduced amount of the kernel weight, starch and protein. Starch biosynthesis genes in nacRNAi mutants are less expressed than those in normal control. Authors carried out the Dual-Luciferase Reporter (DLR) assay in Arabidopsis protoplast through testing the LUC activity driven by both Bt2 promoter and 16-kDa g-zein promoter in the present of the NAC128 and NAC130 separately. They found both NACs increased LUC activity but the activity was higher in NAC130 than in NAC128. Later combined with the Electrophoretic Mobility Shift assays (EMSA) experiment, Zhang et al. identified a cis-element binding site ACGCAA for both transcription factors. Transcriptome analysis found thousands of differential expression genes in both nacRNAi lines, and several carbohydrate metabolic pathways transcripts were down-regulated. Both Y2H and BiFC showed no interaction between the ZmNAC128 and ZmNAC130. Fang Bai, 2019

7/2019 Damon Lisch
Fu, FF; Dawe, RK; Gent, JI. 2018. Plant Cell. 0:doi: 10.1105/tpc.18.00053
   Loss of RNA-directed DNA methylation in maize chromomethylase and DDM1-type nucleosome remodeler mutants

Sequence Reads can be found in NCBI SRA database under the accession SRP127627.

One distinction between plants with large genomes such as maize and those with small genomes such as arabidopsis is the impact of mutants that alter widespread patterns of DNA methylation, particularly those that effect constitutive heterochromatin, such as the chromomethyltransferases (CMTs) and decreased DNA methylation1 (ddm1). In Arabidopis, these mutations are fully viable, likely because Arabidopsis has a limited quantity of heterochromatin that is largely restricted to pericentromeres. In contrast, maize has heterochromatin distributed throughout its genome. Likely as a consequence of this, mutations of the maize homologs of the CMTs DDM1 are inviable in maize. In maize, boundaries between heterochromatin are marked by CHH islands, which are the product of a canonical RNA-directed DNA methylation pathway. Unlike mutants such as ddm1, mutations of maize genes required for RdDM have a minimal effect (with some notable exceptions) on plant phenotype. Because cmt1 and ddm1 mutants are inviable, it has been difficult to extend observations made in arabidopsis to the much more complex maize genome. Fu et al. have found a work around by examining mutant developing embryos and endosperms prior to the death of these plants. In addition to the expected effects of ddm1 and cmt1, the authors observed a dramatic decrease in CHH islands, along with their associated 24 nt small RNAs, along with a dramatic increase in 22 and 21 nt small RNAs derived from heterochromatin that failed to trigger DNA methylation. The authors suggest a model, in which widespread activation of heterochromatin in maize ddm1 and cmt results in recruitment of components of the RNA directed DNA methylation pathway, which dilutes prevents these proteins from participating in their normal function of maintaining CHH islands near genes. Because RdDM is not required for normal maize development, it is unlikely that the loss of normal patterns of RdDM in the ddm1 and cmt mutants are responsible for the inviability of these mutants, so it remains unresolved as to why they are inviable in maize and viable in Arabidopsis. It also remains to be seen the extent to which these mutants effect the global activity of TEs in the maize genome, although the authors do show that the residual Mutator activity in the UniformMu lines is enhanced in the cmt mutants. Damon Lisch, 2019

7/2019 Sarah Hake
Lunde, C; Kimberlin, A; Leiboff, S; Koo, AJ; Hake, S. 2019. Communications Biology 2:114
   Tasselseed5 overexpresses a wound-inducible enzyme, ZmCYP94B1, that affects jasmonate catabolism, sex determination, and plant architecture in maize

Transcriptomic data for 10mm tassel RNA-Seq of Ts5/+and normal siblings are available at the NCBI sequence read archive (SRA) under the accession code PRJNA495059.

Tasselseed5 (Ts5) is a classic dominant mutant with a feminized tassel similar to the recessive ts1 and opr7opr8 in the jasmonic acid pathway. Positional cloning and transcriptomics identified an overexpressed gene homologous to a cytochrome P450 in the CYP94B subfamily as Ts5. This enzyme catalyzes the oxidation of bioactive jasmonate to inactive compounds. Consistent with the identity of the gene, jasmonate profiles were altered in the tassel and in wounded leaves of Ts5 mutants. Sarah Hake, 2019

6/2019 Carolyn Rasmussen
Dawe, RK, et al. 2018. Cell. 173:doi: 10.1016/j.cell.2018.03.009
   A kinesin-14 motor activates neocentromeres to promote meiotic drive in maize

Heterochromatic knobs are rapidly pulled towards spindle poles by a group of minus-end directed Kinesin-14s causing meiotic drive. Interestingly, these ~8 tandemly arrayed kinesins, called KINESIN DRIVER (KINDR) were found clustered in a 1 Mb region of abnormal chromosome 10 (Ab10). RNA sequencing of Ab10 and a line with a deletion of the Ab10 distal tip was used to identify these kinesins. Three independently derived mutants that lost meiotic drive were epialleles that contain high levels of local DNA methylation that reduced all Kindr gene expression. The highly duplicated region containing the kindr locus would make this rare type of epigenetic mutation or large deletions most likely to remove KINDR function. KINDR localizes to knobs containing a 180 base-pair repeat in vivo and is expressed in mitosis and meiosis. KINDR function, as a fast minus-end directed kinesin, was demonstrated using recombinant KINDR protein in a microtubule gliding assay. Finally, the authors show that when KINDR is active, it promotes uneven transmission of chromosomes containing knobs, impacting overall Mendelian segregation of most maize genes. Finding what KINDR binds, whether DNA or another protein, will shed light on how this interesting meiotic drive element works. Carolyn Rasmussen, 2019

6/2019 Damon Lisch
Su, W; Gu, X; Peterson, TA. 2019. Molecular Plant. 0:doi: 10.1016/j.molp.2019.02.008
   TIR-Learner, a new ensemble method for TIR Transposable Element annotation, provides evidence for abundant new transposable elements in maize genome

Although transposable elements (TEs) are a central component of plant genomes, and can often affect gene expression we have struggled to accurately annotate them, and when they are annotated, it is often with the purpose of masking them in order to simplify analysis of what is considered to be the functional part of the genome. However, there is a growing body of research that suggests that TEs are an important regulatory component of plant genomes. But of course we won't know how important they are until we can accurately identify them. TIR class II elements have been particularly challenging because they lack the long LTRs carried by class I elements. TIR elements may be particularly important with respect to regulation of gene expression because they are often intimately associated with genes. Traditionally, TIR elements have been identified by homology. However this manuscript describes a new pipeline for identifying TIR elements, and the results are striking. Relative to B73 V4, this pipeline identified roughly five times as many TIR TEs and adjusted the total proportion of the maize genome of this class of elements from 0.41% to 4.49%. Remarkably, this is likely to be an underestimate, because the pipeline excludes fractured or partial TEs. As has been noted before, the TEs that were identified are highly polymorphic, suggesting that if they are responsible regulatory or functional changes, it should be possible to use those polymorphisms to test hypotheses. In conjunction with other recently developed methodologies (Anderson et. al, bioRxiv:547398), this pipeline is likely to be an invaluable tool, not just in maize, but in any plant genome. Damon Lisch, 2019

6/2019 Fang Bai
Wang, H, et al. 2019. Plant Cell. 0:doi: 10.1105/tpc.18.00736
   A subsidiary cell-localized glucose transporter promotes stomatal conductance and photosynthesis

The opening and closing of the stomata cells regulate the rate of plant respiration and the photosynthesis. To understand the genetic mechanism of the stomata cell movement and the photo-assimilate, Wang et al. identified a mutant in maize named closed stomata1 (cst1) and map-based cloning this SWEET family gene. cst1 demonstrated early senescence, reduced stomatal conductance, stomatal aperture width, photosynthetic rates and the yield compared to the wild type. In a time-course transcriptome analysis of cst1 and wild type, the authors found that the expression levels of senescence-associated genes were significantly higher in cst1 than in wild type leaves. Metabolome profiling using both liquid chromatography tandem mass spectrometry (LC-MS) and gas chromatography tandem mass spectrometry (GC-MS) showed that the nitrogen remobilization is more active in cst1 than in wild type plants which are consistent with the early senescence in cst1 mutant. CST1 subcellular localization experiment observed that the CST1 protein is a cell membrane-localized glucose transporter. Both the bimolecular fluorescence complementation (BiFC) assay and the complementation of the yeast YSL2-1 mutant strain on wild type and cst1 mutant showed that CST1 is an active glucose transporter, and the mutant significantly impaired the glucose transport activity of CST1. By measuring six major forms of sugar and starch, and examining the expression of carbon starvation marker genes, the authors found that the loss-of-function of CST1 leads to carbon starvation in leaves. The authors further demonstrated and concluded that CST1 mediated the feedback-regulation of photosynthesis by photo-assimilates at the grain-filling stage, and cst1 mutation resulted in reduced stomata opening and the inadequate grain filling. Fang Bai, 2019

5/2019 Damon Lisch
Wittmeyer, KT, et al. 2018. Plant Cell. 0:doi: 10.1105/tpc.18.00546
   The dominant and poor penetrant phenotypes of the maize mutation Unstable factor for orange1 are caused by DNA methylation changes at a linked transposon

The dominant Unstable Orange factor1 was identified decades ago as a modifier of P1 expression, which in turn regulates flavinoid production. Ufo1 has a series of effects, likely independent of changes in p1 expression, including short stature, sugar accumulation, and a generalized stress response. Notably, Ufo1 can modify reverse epigenetic silencing of some alleles of P1, making cloning of Ufo1 of great interest to those interested in this process in plants. Unfortunately, as its name suggests, Ufo1 is unstable, likely due to the fact that it itself is subject to epigenetic silencing. Even worse, its penetrance varies depending on the background, making mapping extremely difficult, and, to top it off, it is located in a lies within a nonrecombining region surrounding centromere 10. However, the phenomenology is interesting enough that this group has persisted for years to identify the allele responsible for this novel phenotype. They have finally done so, and the answer is almost as perplexing as the question. As it turns out, the dominant Ufo1 maps to an allele of a gene (GRMZM2G053177) that is ectopically overexpressed in the mutant, which results in overexpression of P1. Remarkably, it appears that overexpression of Ufo1 is due to transcription initiation from within a CACTA transposon, and Ufo1 is unstable because the CACTA transposon can spontaneously silence, and event that is associated with increased methylation. The bad news is that the gene is either rapidly evolving or easily lost, because homologs of this gene are restricted to the Poaceae. Further, although there are some putative domains in this gene, they are not particularly convincing. Thus, although it is deeply gratifying that a decades old mystery has finally been solved, we are left with a series of other mysteries concerning exactly how Ufo1 does what it does. It will be interesting to see what kind of effects overexpression of homologs of this gene have in other species. Damon Lisch, 2019

5/2019 Sarah Hake
Strable, J; Vollbrecht, E. 2019. Development. 0:doi: 10.1242/dev.171181
   Maize YABBY genes drooping leaf1 and drooping leaf2 regulate floret development and floral meristem determinacy

in this paper, Strable and Vollbrecht examine the inflorescence phenotypes of drooping leaf1 and drooping leaf2. They discovered that drl1 is an allele of indeterminate floral apex (Laudencia and Hake. 2002) and that drl2 enhances the drl1 phenotype. The duplicate drl genes encode YABBY proteins that are expressed in lateral organs and thus function non-autonomously to promote determinacy of the floral apex. Sarah Hake, 2019

5/2019 Fang Bai
Nelms, B; Walbot, V. 2019. Science. 364:52-56
   Defining the developmental program leading to meiosis in maize

Meiosis is an important process for all sexually reproducing organisms such as animals and plants. To study the mechanisms of the meiotic entry in plants, Nelms and Walbot characterized male meiosis and the transcriptome changes in single pre-meiotic and meiotic prophase I cells from maize anthers by the single-cell RNA sequencing. The authors found the transcriptome expression shift in a transition from pre-meiotic to leptotene by calculation of the pseudotime velocity during the early anther development. By checking the marker genes expression in somatic and meiotic mutant cells, they found that the expression of the early prophase genes was cell autonomous. GO term analysis showed the enrichment of chromosomal remodeling and differentiation of the meiotic cytoplasm during the transition of the early meiotic phase. Fang Bai, 2019

5/2019 Carolyn Rasmussen
Huang, YC, et al. 2019. Plant Cell. 0:doi: 10.1105/tpc.18.00966
   Maize VKS1 regulates mitosis and cytokinesis during early endosperm development

VARIED KERNEL SIZE1 (VSK1, Zm00001d018624) is a kinesin-14 microtubule motor protein that is important for mitosis and cytokinesis during endosperm development. VSK1 is a homolog of two other recently described kinesin-14s in maize: KINDR and DV1, and ATK5 in Arabidopsis. As suggested from the name, vks1 mutants have variable kernel size, likely caused by delayed and disrupted cell division in developing endosperm cells. Kernel size variation was observed in several genetic backgrounds and in independently generated mutants, indicating that variability is an inherent phenotype of the mutant. 30% of vks1 mutant pollen was defective, reducing transmission in competitive crosses. Spindles and phragmoplasts were abnormal, with frayed poles and irregular morphology, in developing endosperm. Lagging chromosomes and fragmented nuclei were likely due to disruptions in spindle and phragmoplast organization. Vks1 expression is specific to endosperm and highest during the first few days of endosperm development including cellularization and stages dominated by mitotic activity. Microtubule and nuclear localization was observed when VKS1-GFP was expressed in Nicotiana benthamiana, with nuclear localization mediated by the tail domain and proper microtubule localization mediated by both the motor and coiled-coil domains. When immunolocalization using a VKS1 antibody was used in maize endosperm, VKS1 clearly localized to phragmoplast microtubules and less clearly to other microtubule structures and nuclei. It would be interesting to characterize the in vitro motor activity of VSK1 and connect those functions to this fascinating mutant phenotype. Carolyn Rasmussen, 2019

4/2019 Fang Bai
Sarah Hake
Claeys, H, et al. 2019. Nature Plants. 0:doi: 10.1038/s41477-019-0394-z
   Control of meristem determinacy by trehalose 6-phosphate phosphatases is uncoupled from enzymatic activity

RAMOSA3 (RA3) encodes a trehalose 6-phosphate phosphatase (TPP) that plays a central role in the meristem determinacy. ra3 mutants has increased tassel branching and ectopic branching in ears. RA3 might regulate meristem development through dephosphorylates trehalose 6-phosphate (T6P) to trehalose in maize. To understand the roles of T6P and RA3 in regulating meristem development in maize, Claeys et al. did a series of genetics and enzyme activity experiments. They identified TREHALOSE 6-PHOSPHATE PHOSPHATASE 4 (TPP4) as a redundant paralogue of RA3 by screening for enhanced ear branching through EMS mutagenizing ra3 mutants and CRISPR-Cas9 induced mutation. TPP enzymatic activity experiments and transgenic complementary tests showed that TPP enzymatic activity is not important for the control of branching and the meristem determinacy. Fang Bai, 2019

Ramosa3(ra3) encodes a trehalose 6-phosphate phosphatase and functions to limit indeterminacy in maize inflorescences. Claeys and colleagues searched for genetic modifiers that enhanced the ear branching of the ra3mutant and identified four independent mutations in a ra3paralogue, tpp4. tpp4mutants have no phenotype on their own. By complementing a yeasttppmutant, they discovered that their tpp4mutants ranged in enzyme activity. However, there was no correlation with loss of TPP activity and change in branching of ra3;tpp4double mutants. They engineered a catalytically dead RA3 and it was still able to rescue the mutant phenotype. Thus RA3, which is located in the nucleus, has a separate function in inflorescence branching from regulating levels of T6P. Sarah Hake, 2019

4/2019 Fang Bai
Bai, F, et al. 2019. Plant Cell. 0:doi: 10.1105/tpc.18.00754
   RNA Binding Motif Protein 48 is required for U12 splicing and maize endosperm differentiation

The precision of accurate recognition of splice sites during pre-mRNA processing is fundamental to the expression of eukaryotic genes. This complex process requires sequential and stepwise participation of a number of splicing factors assembled in large molecular and dynamic structure called spliceosomes. There are two classes of introns that were spliced by different spliceosome complexes, U2-type introns spliced by the major spliceosome and U12-type introns spliced by the minor spliceosome. Using maize kernel mutants, Bai et al. discovered that RNA Binding Motif Protein 48 (RBM48) participated in minor intron splicing. Reduced minor intron splicing efficiency causes endosperm cells to delay differentiation and to extend cell proliferation. At the protein level, the authors showed that RBM48 interacts with ZRSR2/RGH3, a known U12 splicing factor, as well as known U2 splicing factors, U2AF1 and U2AF2. All three of these proteins are involved in 3' intron recognition of either U12-type or U2-type introns. They also showed that Maize RBM48 has a conserved interaction with ARMC7. This comprehensive study defines molecular, developmental, and biochemical functions of a novel minor splicing factor. Fang Bai, 2019

3/2019 Matthew Hufford
Wang, B, et al. 2018. Genome Res. 0:doi: 10.1101/gr.227462.117
   A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing

The authors of this paper used single-molecule, long read RNA-seq data to analyze the splicing and transcriptome diversity in 11 agronomically important matched tissues between maize and sorghum to better understand difference in architecture between the two species. The authors identified large number of novel isoforms of protein-coding and non-coding genes in both maize and sorghum. By exploring the similarities and difference in gene expression between comparable tissues in both species, they found that the comparable tissues between species were more likely to be clustered than tissues within a species. They observed sub-genome bias in maize and found that genes in pollen were more highly expressed in sub genome B and genes in endosperm were highly expressed in sub genome A. The authors also conducted evolutionary analysis of the gene expression by calculating the transcriptome age of each tissue in both maize and sorghum and concluded that the transcriptome of reproductive tissues are much younger that of of vegetative tissues. Further, to understand the role of alternative polyadenylation in transcriptome diversification between maize and sorghum, they generated and analyzed high resolution maps of poly(A) sites in both the species. Nancy Manchanda, 2019

3/2019 MaizeGDB Staff
McLoughlin, F, et al. 2018. Nature Plants. 0:doi: 10.1038/s41477-018-0299-2
   Maize multi-omics reveal roles for autophagic recycling in proteome remodelling and lipid turnover

Autophagy is the process within cells that allows the proper disposal and of unwanted components and the efficient recycling of macro- and micro- nutrients. This paper uses transcriptome, proteome, ionome and metabolome profiling of normal and atg12 mutants under different conditions to survey autophagic substrates and their impact on metabolism and development. This integrated multi-omics analysis clearly establishes roles for autophagy in numerous cellular processes in maize under both nutrient-replete and -starvation conditions, and provides a unique resource- comprehensive data sets for the identification of proteins, protein complexes, organelles and processes directly or indirectly under autophagic control. MaizeGDB team, 2019

3/2019 Sarah Hake
Liu, X; Galli, M; Camehl, I; Gallavotti, A. 2018. Plant Physiol. 0:doi: 10.1104/pp.18.00913
   RAMOSA1 Enhancer LOCUS2-mediated transcriptional repression regulates vegetative and reproductive architecture

REL2 is a transcriptional co-repressor originally identified in a ramosa1 enhancer screen. The group found additional alleles of rel2 and analyzed the phenotype in two different inbred backgrounds. rel2 mutants are pleiotropic, affecting male and female inflorescences and stem elongation. Some of the phenotypes, such as absence of ears, are background dependent. They carried out a transcriptional profiling and a yeast two hybrid assay. Molecular characterization of the interactions identified two distinct protein domains. This discovery suggests that REL2 may be important in organizing large transcription factor complexes. Sarah Hake, 2019.

2/2019 Sarah Hake
Tsuda, K, et al. 2017. Plant Cell. 0:doi: 10.1105/tpc.16.00967
   KNOTTED1 cofactors, BLH12 and BLH14, regulate internode patterning and vein anastomosis in maize

In this well written and scholarly report, the role of two BELL1-like homeobox (BLH) transcription factors, BLH12 and BLH14, and their roles in stem development are explored. The authors found that BLH12/14 interact with KNOTTED1 (KN1) in vivo and accumulate in overlapping domains in shoot meristems, young stems, and provascular bundles. They show that blh12 blh14 double mutants fail to maintain axillary meristems (as does kn1 loss of function mutants), and have abnormal tassel branching and precocious internode differentiation that results in dwarfism and reduced number of veins in the stems. The authors propose two roles for BLH12/14 during stem development: (1) maintaining intercalary meristems that accumulate KN1 and prevent precocious internode differentiation and (2) preventing precocious anastomosis of provascular bundles in young stems to ensure the production of sufficient independent veins. Sarah Hake 2019

2/2019 Sarah Hake
Je, BI, et al. 2018. Elife. 7:doi: 10.7554/eLife.35673.001
   The CLAVATA receptor FASCIATED EAR2 responds to distinct CLE peptides by signaling through two downstream effectors

These authors address how multiple inputs can be translated into distinct outputs, specifically in the FEA2 signaling pathway which is involved in meristem development. They isolated mutants in the maize CRN ortholog, ZmCRN, and show that ZmCRN and FEA2 function together in a pathway, and that ZmCRN and CT2 function together in a different pathway, and yet FEA2 physically interacts with both CT2 and ZmCRN. They also test the effect of signal peptides on the FEA2 signally pathway. They address how a single receptor might recognize different signals and transmit them differentially. Their data suggest a novel mechanism in plant receptor signaling, where a single receptor, FEA2, can transmit signals from two different CLE peptides, ZmFCP1 and ZmCLE7, through two different downstream components, ZmCRN and CT2. Their data suggests a new model for meristem size regulation, in which ligand binding can be transmitted by a common co-receptor working with different RLKs coupled to distinct signaling proteins. Sarah Hake 2019

2/2019 Sarah Hake
Zhang, D, et al. 2018. Plant Cell. 0:doi: 10.1105/tpc.17.00791
   GRF-interacting factor1 (gif1) regulates shoot architecture and meristem determinacy in maize

These authors describe the null mutant phenotype, and cloning of the gene gif1 (growth regulating factor-interacting factor1). Mutants have short internodes and narrow leaves, and are male and female sterile. Interestingly, the tassel is less branched, but the ear becomes branched. In situ hybridizations show expression in floral organ primordia, leaf margins and the vegetative meristem, consistent with mutant phenotypes. RNAseq and ChIPseq on tassels showed that gif1 regulates cell cycle, inflorescence development and hormone-related genes. Many of the targets and differentially expressed genes are known through their mutant phenotype, for example terminal ear1, ramosa2 and unbranched3. Yeast two hybrid analysis showed that GIF1 interacts with 13 of 16 GRF proteins tested. The authors propose that diverse GIF1-GRF complexes are established in shoot apical meristems to promote leaf and internode development, in the intercalary meristems to promote cohesive growth, and in axillary meristems to maintain determinacy. Sarah Hake 2019

1/2019 MaizeGDB Staff
Springer, NM, et al. 2018. Nature Genetics. 0:doi: 10.1038/s41588-018-0158-0
   The maize W22 genome provides a foundation for functional genomics and transposon biology

The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, the authors have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. They show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies. Annotation of the genome has been achieved using RNA-seq analysis, differential nuclease sensitivity profiling and bisulfite sequencing to map open reading frames, open chromatin sites and DNA methylation profiles, respectively. Collectively, the resources developed here integrate W22 as a community reference genome for functional genomics and provide a foundation for the maize pan-genome.

1/2019 MaizeGDB Staff
Han, XW, et al. 2019. Nature. 0:doi: 10.1038/s41586-018-0857-9
   A kiwellin disarms the metabolic activity of a secreted fungal virulence factor

The biotrophic fungus Ustilago maydis causes smut disease in maize (Zea mays) plants by secreting numerous virulence effectors that reprogram plant metabolism and immune responses. The secreted fungal chorismate mutase Cmu1 presumably affects biosynthesis of the plant immune signal salicylic acid by channelling chorismate into the phenylpropanoid pathway. Here the authors show that one of the 20 maize-encoded kiwellins (ZmKWL1) specifically blocks the catalytic activity of Cmu1. ZmKWL1 hinders substrate access to the active site of Cmu1 through intimate interactions involving structural features that are specific to fungal Cmu1 orthologs. Phylogenetic analysis suggests that plant kiwellins have a versatile scaffold that can specifically counteract pathogen effectors such as Cmu1. The authors reveal the biological activity of a member of the kiwellin family, a widely conserved group of proteins that have previously been recognized only as important human allergens.

1/2019 MaizeGDB Staff
Sun, SL et al. 2018. Nature Genetics pp.doi: 10.1038/s41588-018-0182-0
   Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

In this work, the authors report a de novo, high-quality genome assembly of the Mo17 genome using PacBio and BioNano optical-mapping technologies. More than 96.4% of the 2,183-Mb assembled genome can be accounted for by 362 scaffolds in ten pseudochromosomes with 38,620 annotated protein-coding genes. By aligning the B73 and Mo17 genomes, the authors found 9,867,466 SNPs; 1,422,446 small insertions/deletions (indels, length shorter than 100-bp); and more than 25 MB of presence/absence-variation (PAV, length longer than 500-bp) sequences between the two representative maize genomes. Comparative analysis revealed large gene-order and gene structural variations: approximately 10% of the annotated genes were mutually nonsyntenic, and more than 20% of the predicted genes had either large-effect mutations or large structural variations, which might cause considerable protein divergence between the two inbred lines. This study provides a high-quality reference-genome sequence of an important maize germplasm, and the intraspecific gene order and gene structural variations identified should have implications for heterosis and genome evolution.

1/2019 MaizeGDB Staff
Yao, H, et al. 2019. Molecular Plant. 0:doi: 10.1016/j.molp.2018.12.024
   The barren stalk2 gene is required for axillary meristem development in maize

This article reports the cloning and characterization of the barren stalk2 (ba2) mutant of maize, which has a very similar phenotype to barren stalk1 (ba1) mutants, where the ear shoot is always absent (the meaning of the term "barren stalk") and almost no branches and spikelets are produced in the tassel (indicating a "barren inflorescence" phenotype). The BA2 protein contains a protein-protein interaction domain and physically interacts with BA1, a basic helix-loop-helix transcription factor which acts downstream of auxin to control axillary meristem (AM) formation. Characterization of the genetic interaction between ba2 and ba1 demonstrates that ba1 shows a gene dosage effect in ba2 mutants, providing further evidence that BA1 and BA2 act together in the same pathway. The ba2 mutation suppresses tiller growth in the teosinte branched1 mutant, indicating that ba2 also plays an essential role in vegetative AM development. Enhanced phenotype of ba2;bif2 and ba2;baf1 double mutants suggests that ba2 function in parallel and convergent pathways in reproductive AM development with both bif2 (barren inflorescence2) and baf1 (barren stalk fastigiate1). Phylogenetic analysis shows that ba2 is the syntelog and ortholog of LAX2 in rice and identifies co-orthologs in Arabidopsis and other taxa whose function are not yet known.

1/2019 MaizeGDB Staff
Li, YX, et al. 2018. Sci. Rep.. 8:6848
   Increased experimental conditions and marker densities identified more genetic loci associated with southern and northern leaf blight resistance in maize

Southern leaf blight (SLB) and northern leaf blight (NLB) are the two major foliar diseases limiting maize production worldwide. However, there are no genes causing complete immunity to these two foliar diseases. Instead, quantitative disease resistance (QDR) has been widely used to oppose these two diseases in maize breeding programs. Using a nested association mapping (NAM) population with 5000 RILs obtained from 25 crosses with a common parent (B73), the genetic architecture of SLB and NLB resistance has been analysed. The results demonstrated that resistance of SLB and NLB is predominantly determined by numerous loci with small additive effects. To further the study if these leaf blight resistance, the authors in this report expanded the phenotyping environments from the United States (US) to China, and increased the marker densities from 1106 to 7386 SNPs for linkage mapping, and from 1.6 to 28.5 million markers for association mapping. They identified 49 SLB and 48 NLB resistance-related unique QTLs in linkage mapping, and multiple loci in association mapping with candidate genes involved in known plant disease-resistance pathways. Furthermore, an independent natural population with 282 diversified inbred lines were sequenced for four candidate genes selected based on their biological functions. Three of them demonstrated significant associations with disease resistance. These findings provide valuable resources for further implementations to develop varieties with superior resistance for NLB and SLB.

1/2019 MaizeGDB Staff
Bilinski, P, et al. 2018. PLoS Genetics. 14:e1007162
   Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays

While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. In this article the authors report parallel changes in intraspecific genome size and repeat content of domesticated maize landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. The authors combined genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance, and found that population structure alone cannot explain the observed variation, implying that clinal patterns of genome size are maintained by natural selection. There is also evidence of selection on individual heterochromatic knob repeats, likely due to their large individual contribution to genome size. The authors conducted a growth chamber experiment using a population of highland teosinte exhibiting extensive variation in genome size and found find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. A re-analysis of published data of cell counts in maize shoot apical meristems identified a negative correlation between cell production rate and flowering time. Together, these data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes.

12/2017 Lin Li
Ma, SS; Ding, ZH; Li, PH. 2017. BMC Plant Biology. 17:131
   Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response

Co-expression networks have been evidenced to harbor the patterns of transcriptome organization and suggest common biological functions for networked genes. With the advent of Next generation sequencing, tons of transcriptome data have been accumulated, which provides us an unprecedented chance to construct comprehensive co-expression networks for the dissection of gene functions and regulatory relationships. Ma and colleagues have collected a massive RNA-Seq data and constructed a comprehensive co-expression network with 964 gene modules for 20269 genes. These modules are likely to be involved in a series of biological processes. Interestingly, comparative co-expression network analysis illustrated the conservation and divergence of biological pathways between species. This study provides a sound genomic resources potentially for the future functional studies in maize. Lin Li, 2017

Data Can be found here:

12/2017 Ruben Rellan-Alvarez
Wang, L, et al. 2017. Genome Biol. 18:215
   The interplay of demography and selection during maize domestication and expansion

After domestication in the Balsas River Basin the current state of Guerrero in Mexico, maize colonized a variety of different environments with very different conditions than its original humid, subtropical habitat. While the evolutionary and genetic processes that occurred during maize domestication have been studied in detail, local adaptation of maize to new environments have received much less attention. In this paper, Li Wang and collaborators studied how demographic history and selection shaped maize diversity during maize spread across the Americas. The authors found that maize experienced severe declines in effective population size due to domestication bottlenecks and serial founder effects, the latter, is particularly significant in Andean landraces. On the other hand, the wild relative teosinte parviglumis experienced population growth. This has led to a higher number of deleterious alleles in maize when compared with teosinte. Introgression from another teosinte (teosinte mexicana) that is prevalent in highland Mexico reduced the effect of deleterious alleles in the maize populations like highland Mexico, Guatemala and South West US where maize was able to hybridize with this highland teosinte. This study highlights the opportunity to explore teosinte genetic diversity to incorporate beneficial alleles into modern maize breeding pools and provides a foundational study to understand the evolutionary processes that allowed maize to colonize and be cultivated all around the globe. Ruben Rellan, 2017

12/2017 Fang Bai
He, Y, et al. 2017. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1713225114
   Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize

Meiotic recombination is a key reason for the genome stability and genetic variation in plants and animals. Meiotic recombination is beginning with the forming double-strand breaks (DSBs). Maize has a 2500 Mbp genome and a large distribution of transposons and repetitive sequences. In this paper, He et al. Mapped meiotic DSBs hotspots to the maize reference genome by using the chromatin immunoprecipitation (ChIP) combined with the sequencing of the segments on the Illumina platform. They found that DSB hotspots were around 1.2 kb long and spreaded on the maize genome randomly with the majority of DSB hotspots were located in repetitive DNA, primarily Gypsy retrotransposons. Furthermore, the authors conducted micrococcal nuclease digestion of chromatin and immunocolocalization of H3K4me3 marks and RAD51 foci in a maize meiocyte at zygotene to search for factors controlling DSB locations. They found that DSBs are formed at nucleosome-free and DNA-hypomethylated sites in maize. In addition, He et al. identified a 20-bp-long GC-rich degenerate DNA sequence motif in about 72% of genic DSB hotspots, but not in the repetitive DNA hotspots. The authors also investigated the relationship between the DSB distributions with the chromosomal cross overs (CO) distributions based on the recombination data from the maize Nested Association Mapping. Fang Bai, 2017

12/2017 Jason Wallace
Gage, JL, et al. 2017. Nature Communications 8:1348
   The effect of artificial selection on phenotypic plasticity in maize

Phenotypic plasticity refers to how an organism can adjust its growth based on its environment. In agriculture, this most often manifests as gene-by-environment interaction (GxE). Plasticity / GxE can complicate crop breeding because performance in one environment does not necessarily predict performance in another, although breeders can also exploit it to create lines well suited to particular environments. Gage et al. investigated phenotypic plasticity in the maize Genomes to Fields dataset to determine if modern breeding has selected for or against phenotypic plasticity. They found that regions of the genome that were selected for temperate grain production show less contribution to GxE for yield, indicating that modern breeding has selected against plasticity in favor of yield stability across environments. A similar analysis of height showed no such selection. Genetic regions associated with plasticity were also enriched in the 5 kb upstream of genes, implying that regulatory variation has an outsize contribution to phenotypic plasticity and GxE. Jason Wallace, 2017

11/2017 Jason Wallace
Diepenbrock, CH, et al. 2017. Plant Cell. 0:doi: 10.1105/tpc.17.00475
   Novel loci underlie natural variation in vitamin E levels in maize grain

The authors investigated tocochromanol synthesis in all 5000 members of the maize Nested Association Mapping population. Tocochromanols are important antioxidants in seeds that contribute to seed viability, and in the diet they constitute a source of Vitamin E. The authors identified 52 QTLs for one or more tocochromanol traits, including 14 that resolve to individual genes. Six of these genes have activities not before associated with tocochromanols, including chlorophyll biosynthesis genes. Many of the QTL have a significant impact on the levels of one or more tocochromanol compounds, including showing epistatic interactions. Understanding how these genes interact in grain tocochromanol synthesis should enable them to be used in biofortification breeding schemes. Jason Wallace, 2017

11/2017 Fang Bai
Dong, Z, et al. 2017. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1714960114
   Ideal crop plant architecture is mediated by tassels replace upper ears1, a BTB/POZ ankyrin repeat gene directly targeted by TEOSINTE BRANCHED1

The teosinte branched1 (tb1) encodes a class II TCP transcription factor which is known to repress the tillers and aerial axillary branches development. Teosinte is the wild ancestor of maize which has highly branched tillers and aerial parts. Domesticated maize contains a natural gain of function allele of tb1 which reduced the branch and increased the yield. In this paper, authors screened the mutants with the similar phenotype of tb1. Dong et al. cloned the gene tassels replace upper ears1 (tru1) by chromosome walking and found that TRU1 encodes an ankyrin repeat domain gene containing a BTB/POZ motif. Using genetic cross of tb1 and tru1 mutants combined with the immunolocalization experiments, they found that TRU1 and TB1 function in the same pathway. Further chromatin immunoprecipitation (ChIP) and qPCR confirmed the direct interaction of the BTB/POZ domain ankyrin repeat protein and TB1. The significant of this paper is that the authors found a genetic mechanism of the domesticating of teosinte to modern crop. Fang Bai, 2017

11/2017 Lin Li
Li, X, et al. 2017. Nature communications. 8:991
   Single nucleus sequencing reveals spermatid chromosome fragmentation as a possible cause of maize haploid induction

The doubled haploid (DH) technology enables generating completely homozygous lines in just two generations and, thus, has been widely used in modern genetics and breeding. However, the molecular mechanisms of the core technique ��� haploid induction is largely unclear. Li and colleagues employed an very sophisticated technique combining single nucleus isolation and high-throughput sequencing, and traced the genomic structure variation during double fertilization after the pollination of inducer pollen. This study provides a detailed molecular view of spermatid chromosome fragmentation during haploid induction, which supports the hypothesis of fertilization first followed by chromosome elimination since paternal DNA fragments. This study largely furthered our understanding of molecular mechanism of haploid induction in plants. Lin Li, 2017

10/2017 Jason Wallace
Bedoya, CA, et al. 2017. PLoS One. 12:e0173488
   Genetic diversity and population structure of native maize populations in Latin America and the Caribbean

The authors profiled 194 maize populations from across Latin America and the Caribbean to characterize the relationships among these accessions. The landraces fell into three main groups: one that includes Mexico and the southern Andes (due to both pre- and post-Columbian movment of germplasm between the two), a lowland Mesoamerican and Caribbean group, and an Andean group that has remained relatively isolated from the other two. Each group was further divided into subclusters based on within-group genetic diversity, with 3-9 subclusters per group. The authors also relate the patterns of variation to proposed routes of human migration through Latin America. Jason Wallace, 2017

10/2017 Ruben Rellan-Alvarez
Kusmec, A et al. 2017. Nature Plants 3:715-723
   Distinct genetic architectures for phenotype means and plasticities in Zea mays

Plasticity, the ability to express different phenotypic responses to varying environmental conditions and robustness, and the ability to maintain a developmental program in a diverse set of environments are conflicting choices that plants need to address. Plasticity as a trait is under genetic control and variation QTLs have been studied in a number of species and is of great interest for plant breeders that want to understand what are the genetic components explaining trait plasticity over different environments. In this paper, Kusmec and collaborators used the 5000 RILS of the NAM mapping population and measured 23 agronomic traits in multiple environments. Using a Finlay-Wilkinson regression that calculates a regression line for a trait in a given line and environment and compares it with the average value of all the lines for that trait in that given environment. Using this approach the authors were able to dissect the genetic components explaining plasticity and mean values of all the traits they evaluated and show that different genes control plasticity and mean values and open the opportunity to be able to breed for both plasticity and robustness. Ruben Rellan, 2017

10/2017 Lin Li
Li, Q, et al. 2017. Plant Cell. 0:doi: 10.1105/tpc.17.00576
   The maize imprinted gene Floury3 encodes a PLATZ protein required for tRNA and 5S rRNA transcription through interaction with RNA polymerase III

The authors cloned the classical mutant floury3 and validated that an Asn to His replacement in PLATZ (plant AT-rich sequence- and zinc-binding) protein is the causal mutation. Genetic experiments indicated that Floury3 is a specially expressed in maize starchy endosperm cells and regulated by genomic imprinting. Floury3 interacts with PRC53 and TFC1, which are the key components of the RNA polymerase III (RNAPIII) transcription complex. The causal mutation in Floury3 could impair the function of RNAPIII, which reduces the levels of many tRNAs and 5S rRNAs, and further lead to defects in endosperm development and storage reserve filling in maize floury3 seeds. It is the first report on the genetic and functional role of PLATZ transcriptional factors in plants. Lin Li, 2017

10/2017 Fang Bai
Chen, JY, et al. 2017. Plant Cell. 0:doi: 10.1105/tpc.17.00099
   Zygotic genome activation occurs shortly after fertilization in maize

With the rapid development of the global transcription study, thousands of genes were reported to involve in the embryogenesis in flowering plants. However, the study of the onset of zygote genome activation (ZGA) in crops is limit. In this paper, Chen et al. generated transcripts from the male and female gametes, and the zygotes at the different hours after pollination in maize. They compared the maize transcriptomes to those published RNA-Seq data from rice sperm and egg cells, and found the conserved genes involved in the gametogenesis and embryogenesis. To characterize the onset of ZGA, they analyzed the transcription profiles of the sperms, eggs and the zygotes at early stages, and found that ZAG happened shortly after the fertilization. They further studied the transcription factors in gametes and zygotes, and examined some homeodomain genes that activated in embryo patterning. Since the cell cycle regulation during zygote development, the authors investigated the expression patterns of 443 important cell cycle regulator genes in games and zygotes and determine the timing of zygote development in maize. In addition, they analyzed the auxin regulated genes and some cell signaling genes in early embryo patterning in maize. The significance of this paper is that they detailed analyzed the timing of zygote development and generated RNA-Seq transcriptome profiles of gametes and zygote cells which will provide the comprehensive dataset for the research community and future crops study. Fang Bai, 2017

9/2017 Fang Bai
Yang, Q, et al. 2017. Nature Genetics. 0:doi: 10.1038/ng.3919
   A gene encoding maize caffeoyl-CoA O-methyltransferase confers quantitative resistance to multiple pathogens

Maize is one of the most important economic plants in the world and the major crop in U.S. However, fungal disease severely damaged the plants during the plant development and largely reduced the crop yields. Recently, several disease-resistance quantitative trait loci (QTL) in maize have been studied and seven maize disease-resistance genes were identified and published. One of the disease-resistance QTL named qMdr9.02 is on the chromosome 9 in maize. qMdr9.02 has been shown to be associated with resistance to three foliar fungal diseases in maize: southern leaf blight, gray leaf spot and northern leaf blight. In this paper, Yang et al. mapped the B73qMdr9.02 to a small window around 100-kb interval on chromosome 9 by repeated backcrossing of NC292 to B73 with marker-assisted selection. The authors did specific association analysis and expression experiment for the candidate genes in qMdr9.02 region. With the help of transgenic lines and the disease resistant experiments, they identified a caffeoyl-CoA O-methyltransferase (CCoAOMT) gene,ZmCCoAOMT2, is the gene that give the resistance effect at qMdr9.02. By using liquid chromatography-mass spectrometry (LC-MS), the authors found that ZmCCoAOMT2 controls metabolite levels in the phenylpropanoid and lipoxygenase pathways. In addition, ZmCCoAOMT2 may function in disease resistance by suppressing the program cell death. This significant discovery indicates a way in the future to improve the crop disease-resistance and increase the crop yield. Fang Bai, 2017.

9/2017 Jason Wallace
Swarts, KL, et al. 2017. Science. 357:512-515
   Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America

Maize arrived in the lowlands of what is now the Southwestern United States ~4000 years ago but did not achieve widespread cultivation in the highlands until ~2000 years later. This delay is hypothesized to be due to poor adaptation of tropical maize to the short growing season of upland areas. Swarts et al. tested this hypothesis by sequencing ancient DNA from right after upland maize cultivation became widespread and using modern maize landraces and inbred lines to predict the phenotypes of these ancient varieties. They found that the ancient maize was partly adapted to earlier flowering (faster than tropical varieties but not as fast as modern fast-flowering varieties). The ancient varieties were also predicted to be shorter and bushier (with more extensive tillering) than modern varieties. The segregation patterns of regions that appear to be selected for flowering indicate that shorter flowering was selected by combining standing variation rather than from novel mutations. Jason Wallace, 2017

9/2017 Lin Li
Leng, PF, et al. 2017. Molecular Plant. 0:doi: 10.1016/j.molp.2017.07.013
   Auxin binding protein 1 reinforces resistance to sugarcane mosaic virus in maize

After cloning the resistant gene ZmTrxh (Scmv1) to Sugarcane mosaic virus in maize, the collaboration by Mingliang Xu Lab from China Agricultural University and Thomas Lübberstedt Lab from Iowa State University published the work on cloning ZmABP1, which is the other resistant gene to Sugarcane mosaic virus. There are two major QTLs conferring the resistance to Sugarcane mosaic virus in maize. ZmABP1 is the functional gene of Scmv2. Moreover, ZmABP1 could enhance the resistant effect of ZmTrxh. ZmABP1 encodes a Auxin Binding Protein. The causal SNP mutation in ZmABP1 could result in the differentially expression of ZmABP1, which leads to the resistance to Sugarcane mosaic virus in maize. The discovery of ZmABP1 and ZmTrxh furthers the understanding of resistance mechanism to virus in plants and will benefit maize breeding on the resistance selection. Lin Li, 2017

This paper shows that the gene scmv2 is the same as the gene abp1. That is, abp1 is the gene responsible for scmv resistance contributed by scmv2. This was confirmed by the authors to MGDB curator staff. The gene model is GRMZM2G116204

9/2017 Ruben Rellan-Alvarez
Studer, AJ et al. 2017. Genetics 207:755-765
   Selection during maize domestication targeted a gene network controlling plant and inflorescence architecture

There are currently no comments for this article.

8/2017 Ruben Rellan-Alvarez
Zhang, Y et al. 2017. Plant Cell pp.doi: 10.1105/tpc.17.00354
   Differentially regulated orthologs in Sorghum and the subgenomes of maize

There are currently no comments for this article.

8/2017 Fang Bai
Kim, Eun-Deok, et al. 2017. Sci. Rep.. 7:3838
   Spatio-temporal analysis of coding and long noncoding transcripts during maize endosperm development

Endosperm is a persistent structure and the main food resource for the embryo during the maize seed development. Endosperm has four cell types: aleurone (AL), starch endosperm (SE), embryo surrounding region (ESR), and basal endosperm transfer layer (BETL). In this paper, Kim et al. studied the coding and long noncoding transcripts from AL, SE and BETL at three different developmental stages. Based on the RNA-seq analysis, they found that both coding and non-coding transcripts were more abundant in BETL than other two cell types, and they played regulatory roles in the endosperm cell differentiation. The authors further classified spatio-temporal transcripton clusters and analyzed their functions using GO term analysis. They studied the spatio-temporal epigenetically regulation of imprinting and found that maternally expressed genes (MEGs) enriched in AL and BETL, and paternally expressed genes (PEGs) enriched in BETL. Kim et al. also examined the enrich region of H3K27me3, an epigenetic marker, by chromatin immune-precipitation (ChIP) followed by sequencing. They showed that the transcripts from H3K27me3-enriched loci were over-represented in BETL transcriptom. Fang Bai 2017

8/2017 Jason Wallace
Tan, BC, et al. 2017. Genetics. 206:135-150
   Structure and origin of the White Cap locus and its role in evolution of grain color in maize

White Cap is a dominant genetic locus that turns yellow maize endosperm white. The authors localized the Wc locus to a tandem duplication of up to 23 copies of a Carotenoid clevage dioxygenase 1 gene (Ccd1). The authors propose a model where a duplication first created a second copy of Ccd1 and surrounding genes, followed by tandem expansion due to unequal crossing-over between Tam3L transposons in the new cluster. Although Wc is most visible in yellow-endosperm maize the alleles are most common in white varieties (and absent in teosinte). The authors propose that Wc intensifies the whiteness of already white kernels, which could have been the basis for human selection. Jason Wallace, 2017

8/2017 Lin Li
Strable, J, et al. 2017. Plant Cell. 0:doi: 10.1105/tpc.16.00477
   Maize YABBY genes drooping leaf1 and drooping leaf2 regulate plant architecture

Ideal plant architecture is a key contributor to high yield of modern maize production. Accompanied with the increase of maize yield, maize leaf angle showed a vital change, which made an ideal canopy structure for high density of maize planting. However, the genetic architecture has not been fully addressed. In this study, Strable and colleagues uncovered two drooping leaf mutants, which showed pleiotropic mutations affecting leaf length and width, leaf angle, and internode length and diameter. A series of genetic experiment, including bulked analysis, fine-mapping, and allelism test etc, identified the causal genes, which are paralogous YABBY genes. Following functional analyses such as histological, scanning electron microscope analyses, RNA hybridization etc, demonstrated that drl genes control elaboration of leaf patterning and further shape leaf architecture in maize. Quantitative analysis in NAM-RIL population also validated that drl loci had the quantitative variation for leaf and stem traits, indicating that these drl loci have not been fixed during the modern breeding and will be good targets for the future selection in maize breeding. Overall, this study provides us a solid link for the function of YABBY genes in the shaping of maize architecture, and furthers our understanding of the genetic architecture of maize plant architecture. Lin Li, 2017

7/2017 Jason Wallace
Canas, RA, et al. 2017. Plant Cell. 0:doi: 10.1105/tpc.16.00613
   Exploiting the genetic diversity of maize using a combined metabolomic, enzyme activity profiling, and metabolic modelling approach to link leaf physiology to kernel yield

The authors used a panel of 19 European and American maize lines to investigate patterns among metabolites, enzyme activity, and metabolic flux. Leaf metabolites and enzyme activities were assayed during vegetative (7-8 leaf stage) and grain-filling (15 days after silking) growth. The authors performed clustering of lines based on different metabolic or enzymatic measures, and also performed metabolic modeling and cluster analysis to identify differences among lines and which of these differences may influence yield. The authors find many correlations among traits, although with only 19 lines it is questionable how many of them would replicate across a larger panel. Ultimately, this paper provides some very interesting descriptive analysis of metabolism in diverse maize lines, though it remains to be seen how useful the derived predictions will be. Jason Wallace, 2017

7/2017 Lin Li
Gent, JI; Wang, N; Dawe, RK. 2017. Genome Biol. 18:121
   Stable centromere positioning in diverse sequence contexts of complex and satellite centromeres of maize and wild relatives

Centromeres, the gene desert, seem mysterious to many scientists given its ultra-complex composition and structure. In this paper, the authors have conducted a comparative genomic analysis based on CenH3 ChIP-Seq data maize and its wild relatives Z. mays parviglumis, Z. mays mexicana, and Z. mays huehuetenangensis, defined the complex centromeres, and revealed the stability of centromere positioning. The study provides us evidence to reject the hypothesis that complex centromeres are an outcome of cultivation and inbreeding, furthers our understanding of centromeres at a population level. Lin Li, 2017

7/2017 Fang Bai
Jiao, YP, et al. 2017. Nature. 0:10.1038/nature22971
   Improved maize reference genome with single-molecule technologies

This paper announces Zm-B73-REFERENCE-GRAMENE-4.0, also known as B73 RefGen_v4, AGPv4. The annotation set is called Zm0001d. This paper was officially published June 12, 2017. From this date the sequence is no longer under the Toronto agreement.

Due to the large and complex identity, it is always a challenge to assemble the maize genome accurately. The old version of maize genome was assembled by using the Sanger Sequencing which was composed of more than 100,000 small contigs and missed some complex repeat regions. In this paper, the new version of maize genome was assembled by Jiao et al. based on a 65x Single-Molecule Real-Time Sequencing (SMRT) and high-resolution optical mapping. This version of B73 genome is composed of 2,958 contigs, which significantly increase the contig length and notably reduce the assemble errors. Fang Bai 2017

6/2017 Lin Li
Tai, F, et al. 2016. Plant Cell, Tissue and Organ Culture (PCTOC). 124:459-469
   ZmCIPK8, a CBL-interacting protein kinase, regulates maize response to drought stress

Plants/crops are more likely to encounter harsh environments under the global climate change. Identification of functional genes underlying stress tolerance is a key step for the improvement of stress tolerance during plant breeding. It has been reported that CBL-interacting protein kinases play an important role in plant stress tolerance. This study has cloned a novel CIPK gene. Subsequent bench works including expression analysis, Yeast two-hybrid assay, BiFC, and plant transformation, provided the evidences that it may be involved in plant response by regulating stress-related genes such as ZmCBL1, ZmCBL4 and ZmCBL9 etc. This paper has been nominated as one of the 180 groundbreaking articles that would change our world by Springer Nature Editors-in-Chief in 2016. Lin Li, 2016

cipk8 expression is greatly increased in drought conditions. Overexpression of maize cipk8 in tobacco enhances tobacco's resistance to drought stress

6/2017 Ruben Rellan-Alvarez
Lee, C-R, et al. 2017. Nature Ecology and Evolution. 1:119
   Young inversion with multiple linked QTLs under selection in a hybrid zone

Chromosomal inversions are chromosomal rearrangements that can span several Mb and have been described in several organisms from Drosophila to maize. Inversions suppress recombination and can favor local adaptation and speciation if they capture favorable alleles since. Its not clear though if favorable alleles accumulate in older inversions or, as the Kirkpatrick Barton model proposes, inversions capture chromosomal blocks that contain pre-existing adaptive alleles. In this paper, Cheng-Rui Lee, show that in a hybrid speciation zone with ecologically different subspecies (East and West) of Boechera stricta a young inversion arose after the last glaciation, quickly reached high frequency and shows signs of positive selection. The authors used a cross of collinear haplotypes to show that the inversion carries several QTLs that influence several phenological and developmental traits and controls high percentages of the phenological differences between the two subspecies. In summary this paper shows that inversions can capture pre-existing, favorable, linked QTLs during initial steps of speciation. Ruben Rellan, 2017

Complete author list: Cheng-Ruei Lee, Baosheng Wang, Julius P. Mojica, Terezie Mandáková, Kasavajhala V. S. K. Prasad, Jose Luis Goicoechea, Nadeesha Perera, Uffe Hellsten, Hope N. Hundley, Jenifer Johnson, Jane Grimwood, Kerrie Barry, Stephen Fairclough, Jerry W. Jenkins, Yeisoo Yu, Dave Kudrna, Jianwei Zhang, Jayson Talag, Wolfgang Golser, Kathryn Ghattas, M. Eric Schranz, Rod Wing, Martin A. Lysak, Jeremy Schmutz, Daniel S. Rokhsar & Thomas Mitchell-Olds.

6/2017 Jason Wallace
Lorant, A et al. 2017. PLoS One 12:e0184202
   The potential role of genetic assimilation during maize domestication

Most studies of crop domestication compare existing crops to their existing wild relatives, since archaeological remains and ancient DNA are both extremely rare. To investigate the process of maize domestication, Lorant et al. grew maize and teosinte under environmental conditions similar to those expected to be present at the time of maize domestication. Under these conditions, teosinte exhibits several maize-like traits, and the authors propose that during domestication these traits became genetically fixed (a process called "genetic assimilation"). They performed transcriptome analysis of maize and teosinte under both ancient and modern climactic conditions and found ~2000 genes that altered expression in teosinte but showed no such change in maize. These results imply that these genes are no longer environmentally responsive but instead are genetically fixed, at least under the conditions tested. Although some of these genes coincide with previously identified selective sweeps, as a group they are not enriched for domestication loci, so other processes may also have been at work. Jason Wallace, 2017

This paper discovers several thousand differentially expressed genes between teosinte and maize in an environment similar to the time of early domestication (Early Holocene). Some genes were differentially expressed only in teosinte, suggesting genetic assimilation may have occured. They include the following auxin and auxin response genes:SAUR33 (GRMZM2G460861), auxin efflux carrier PIN5a (GRMZM2G025742), AUX IAA (GRMZM2G057067) and a PAR (GRMZM2G423863). Also with evidence of assimilation were TCP (TEOSINTEBRANCHED1/ CYCLOIDEA/PCF) transcription factor 44 (GRMZM2G089361), ZOG3 (GRMZM2G338465), gibberellin and ABA regulators GRMZM2G301932 and GRMZM2G338465, and nitrate reductase NADH1 (GRMZM2G568636) and ferredoxin1 (GRMZM2G043162). These are the only gene models mentioned in the paper.

These USDA teosinte accessions were used in this study: PI 384062, PI 384063, PI 384071, PI 566692

These USDA maize accessions were used in this study: Ames 19288 Oh43, PI 550473 B73, NSL 30053 W22, PI 558532 Mo17

6/2017 Fang Bai
Garcia, NS et al. 2017. Proc Natl Acad Sci, USA 114:5165-5170
   Maize defective kernel mutant generated by insertion of a Ds element in a gene encoding a highly conserved TTI2 cochaperone

The maize transposable elements Ac/Ds have been widely exploited and used in maize genetic research since it was discovered by Barbara McClintock over 50 years ago. Recently, Ac/Ds were modified by tagging the Ds elements with a green fluorescent protein (GFP) and editing the 5' and 3' sites with the Ac recognition sequence (Dsg). In this paper, Garcia et al. isolated and characterized an embryo-lethal mutant dek38-Dsg from Dsg collection. The authors took the advantages of the Dsg system to sort the wild types, heterozygotes and mutant seeds. The reciprocal cross between the mutant and WT showed the reduced male transmission. Garcia et al. found that dek38 encodes a TTI2 (Tel2-interacting protein 2) molecular cochaperone which is the homolog of yeast and Mammalian Tie2. They did the yeast two-hybrid experiment and showed that TTI2 interact with maize TTI1 and Tel2 to form the TTT complex which indicates the conserved roles of TEL2, TTI1, and TTI2 in eukaryotes. Fang Bai 2017

6/2017 Fang Bai
Yang, Y-Z, et al. 2017. Plant Physiol. 0:doi: 10.1104/pp.16.01295
   Small kernel2 encodes a glutaminase in vitamin B6 biosynthesis essential for maize seed development

Vitamin B6 is one of the essential nutrients and its active form of pyridoxal 5'-phosphate is a coenzyme involved in several aspects of metabolisms. Recent study showed that Vitamin B6 plays the role in the embryo development in Arabidopsis. In this paper, Yang et al. study the roles of vitamin B6 in embryogenesis and endosperm development in maize. They identified a recessive embryo-lethal mutant small kernel2-1 (smk2-1) from the UniformMu transposon mutagenesis population and cloned smk2 by transposon tagging and sequencing. Yang et al. found that smk2 is a vitamin B6 biosynthetic mutant of maize. The homozygote mutants affected the embryogenesis in maize which is the same as in Arabidopsis, but had fewer effects in endosperm development. smk2 encodes the glutaminase subunit of the PLP synthase. The subcellular localization results showed that SMK2 is located in the cytosol. The authors measured the vitamin B6 contents in the embryo and endosperm of the mutants and their wild type (WT) sibling seeds by HPLC and found that the content of total vitamin B6 was drastically reduced in both embryo and endosperm of mutants compared to the WT. Also, based on the evidences that the maize smk2 partially complements the Arabidopsis pdx2.1 and the yeast MML21 mutant phenotypes, as well as the application of the vitamin B6 partially rescued the smk2 mutant, they concluded that SMK2 functions in vitamin B6 biosynthesis in maize. Fang Bai 2017

5/2017 Jason Wallace
Bian, Y; Holland, JB. 2017. Heredity. 0:doi: 10.1038/hdy.2017.4
   Enhancing genomic prediction with genome-wide association studies in multiparental maize populations

Genomic prediction promises to accelerate crop improvement by letting breeders predict phenotypes from genotypes. Bian & Holland tested how including GWAS-identified markers in genomic prediction schemes would affect prediction using both simulated and real data from the maize Nested Association Mapping population. With oligogenic traits (10 simulated QTL and real disease resistances), including GWAS results significantly increased the accuracy of genomic prediction. However, with polygenic traits (100 simulated QTL and real plant height) prediction accuracy did not improve, and under some circumstances actually dropped. The authors conclude that the proper pipeline for analysis is trait-specific, and exploratory analyses to determine trait architecture would help determine the best methods to use. Their simulated data also revealed a strong coupling between between false discovery rate and power to identify true QTL, so that it was impossible to choose a truly optimal threshold for GWAS analysis. For genomic prediction, however, using the Bonferroni-corrected cutoff worked well. Jason Wallace, 2017

5/2017 Fang Bai
Rosa, M et al. 2017. Plant Cell 29:474-490
   The maize MID-COMPLEMENTING ACTIVITY homolog CELL NUMBER REGULATOR13/NARROW ODD DWARF coordinates organ growth and tissue patterning

Maize leaf is a classic system to study the organogenesis due to its distinct cell division, differentiation, and the pattern formation during the leaf development. One of the main projects in Dr. Sarah Hake lab is to study the genes and their functions underlining the leaf development. In this paper, Rosa et al. characterized a mutant called narrow odd dwarf (nod), which was discovered from EMS screening. The thorough phenotype analysis showed that nod mutants has a pleiotropic phenotypes in both vegetative and reproductive development such as dwarf bushy-like adult plants, reduced leaf dimension, and the abnormal cell division and expansion, etc.. Positional cloning found that nod encodes the maize MCA protein, a PLAC8-containing protein previously annotated as CNR13. Mosaic analysis indicates nod function cell-autonomously at the cellular and organ level. Through the RNA-seq analysis in nod mutant compared to their wild type controls, Rosa et al. demonstrated that the nod involves multiple molecular pathway such as hormone metabolism, phase-change regulation, and pathogen defense etc.. They proposed that nod regulates the cell activities by integrate both intrinsic and environmental cues. Fang Bai 2017.

5/2017 Lin Li
Bouchet, S et al. 2017. Heredity 118:249-259
   Association mapping for phenology and plant architecture in maize shows higher power for developmental traits compared with growth influenced traits

Maize grain yield in US has increased eight-fold in the past 80 years, of which half was contributed by breeding. Although high grain yield per plant is a primary breeding goal, the gain of maize grain yield is largely due to higher plant density. As plant density increased, maize plant morphology has been dramatically altered to optimize lights penetration into the plant canopy. Previous studies usually focused on single or a few morphology traits for the genetic dissection of maize plant morphology variation. Here, the authors assessed the genetic architecture of 24 morphology related traits in a European association mapping panel consisting of 336 diversity maize lines. Association mapping identified 34 QTLs for individual traits and six for trait cluster generated by PCA analysis. Two major observations seem very interesting: one is that only a few (5) QTL were pleiotropic although there was high correlations between these 24 morphology traits; the other is that developmental traits such as tillering, leaf number were likely to be controlled by higher number of detectable QTLs with larger individual QTL effects than growth influenced traits such as Ears per plant, Kernel row number. These results further our understanding of plant morphology diversity, which may benefit maize breeding in the future. Lin Li, 2017

4/2017 Fang Bai
Martinez, P; Luo, A; Sylvester, AW; Rasmussen, CG. 2017. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1619252114
   Proper division plane orientation and mitotic progression together allow normal growth of maize

Symmetrically and asymmetrically cell division contributes to the cell polarity, cell shape and function, tissue formation and organ development. The TANGLED1 (TAN1) is originally identified in maize and function in the proper division plane orientation in dividing cells. In this study, Martinez et al. examined the time-lapse imaging and division-time quantification of the TAN1���YFP on the dividing tan1 cells and their normal sibling cells, and showed that TAN1���YFP was recruited to the division site after the preprophase band (PPB) formation. Their experiment of transformed tan1 with TAN1���YFP fully rescued the mutant phenotype or partial rescued with D-TAN1-13���YFP. The authors also crossed the YFP-TUBULIN into tan1 mutants to show that tan1 mutants had a phragmoplast guidance defect which resulted in the defects in division plane orientation of tan1 mutant. The significance of this research is that the authors directly demonstrated the correct division plane orientation is critical factor for the proper plant growth. Fang Bai 2017

4/2017 Fang Bai
Gault, CM, et al. 2017. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1616173114
   Aberrant splicing in maize rough endosperm3 reveals a conserved role for U12 splicing in eukaryotic multicellular development

There are two types of spliceosomes involved in the RNA slicing in the eukaryotic cells, the major spliceosome of U2-type which will remove the U2-type intron and the minor spliceosome of U12-type which will remove the U12-type intron. Rgh3 is the maize ortholog of the human ZRSR2 RNA splicing factor that is identified several years ago by Dr. A. Mark Settles lab. Rgh3 affects the seed development and plant viability and the endosperm cell differentiation in rgh3 mutants is defective and delayed. In this study, Gault et al. did the RNA-seq in normal and rgh3 seedlings and roots, and tested the minor splicing in rgh3 compared to the normal siblings. The authors showed the disrupt of both the U12 splicing and the localization of the U2AF2 in mutant rgh3 allele which is similar to the human ZRSR2. The results demonstrated the conserved role of the protein RGH3/ZRSR2 across the kingdom. RT-PCR analysis using RNA extracted from total, nuclei, and polysome fractions of normal and rgh3 samples showed that some mis-spliced transcripts in rgh3 are likely to be translated. The significant finding in this study is that the authors showed extensive conservation between maize and human U12-type intron-containing genes. Fang Bai 2017

4/2017 Jason Wallace
Karn, A et al. 2017. G3 7:1157-1164
   Genetic analysis of teosinte alleles for kernel composition traits in maize

Starch, protein, and oil are the three major components of maize kernels and they have been under strong selection during both maize domestication and improvement. Karn et al. used a set of 10 near-isogenic line (NIL) families consisting of 3% teosinte in a B73 background to investigate the effect of ancestral teosinte alleles on kernel composition. They found 8 QTL that significantly affected kernel composition, six of which matched QTL found for the same traits in the maize Nested Association Mapping population (Cook et al 2012, Plant Phys 158:824-834) and two of which are novel. Many allelic effects were stronger in these NILs than in NAM, indicating that teosinte could serve as a source of useful alleles to introgress into modern germ plasm. Jason Wallace, 2017

4/2017 Ruben Rellan-Alvarez
Fustier, M-A, et al. 2017. Mol Ecol. 0:doi: 10.1111/mec.14082
   Signatures of local adaptation in lowland and highland teosintes from whole genome sequencing of pooled samples

Teosinte, the ancestor of maize, grows in a range of environments in M��xico. Teosinte parviglumis (Zea mays ssp parviglumis) is more prevalent in lowland regions while teosinte mexicana (Zea mays ssp mexicana) occupies highland (>2000 masl) territory. Admixture between parviglumis and mexicana can occur at mid-elevations. In this paper, the authors sampled an altitudinal gradient of teosinte populations and the used pooled sequencing populations of low, mid and high elevations. The authors used two population differentiation methods and correlations of allele frequencies with environmental variables to find outlier SNPs that tended to cluster together and 47 candidate regions were identified. The authors were able to recover a previously characterized inversion in chromosome 1. A soft sweep was found in a locus involved in leaf macrohair variation, a phenotype that is characteristic of teosinte mexicana and that is absent in lowland, teosinte parviglumis. Finally several outlier SNPs colocalized with loci involved in root system architecture, heavy metal tolerance and nutrient deficiencies point to a significant role of soil physico-chemichal properties as major drivers of teosinte local adaptation. Ruben Rellan, 2017

4/2017 Lin Li
Zhang, X, et al. 2017. Plant Physiol. 173:1554-1564
   High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth

With increasing demand to accelerate progress in crop breeding for novel traits, the plant research community needs to accurately measure increasingly large numbers of plants and plant traits. Compared with the progress of the large-scale characterization of plant genomes, there is a phenotyping bottleneck hampering progress in both knowledge and application-oriented research in crops. The authors in the paper employed a automatic phenotyping platform to profile over 100 traits across 16 developmental stages in a maize RIL population. Subsequent quantitative analyses of these traits identified ~1000 QTLs underlying agronomic traits and revealed the dynamic genetic architecture of maize plant growth. This study may provide a new strategy to breed plants that can better adapt to low input agriculture and resource-limited environments. Lin Li, 2017

This paper identifies 938 QTLs or 42 investigated phenotypic traits across 16 time points of maize growth

3/2017 Philipp Weckwerth
Waters, AJ, et al. 2016. Plant J. 0:DOI: 10.1111/tpj.13414
   Natural variation for gene expression responses to abiotic stress in maize

The authors are investigating differential gene expression after abiotic stress (cold and heat) in diverse maize inbreds B73, Mo17, Oh43, PH207 and B37. They are putting an emphasis on cis- as well as trans- regulatory elements, as these require concerted action to fully mount abiotic stress responses. For their study, they used 14-day-old maize seedlings. As anticipated a large number of genes were identified that responded differentially to stress. Remarkably, there are also a large number of genes that are different between parental inbred. RNA sequencing was also performed on similar tissues of the F1 hybrids produced by crossing B73 and three other inbred lines (Mo17, PH207, Oh43). The F1 hybrids were further analyzed to evaluate allele-specific transcript abundance. This helped in assessing the abundance of cis- and trans-regulatory variation between genotypes for both steady-state and stress-responsive expression differences. Though cis-regulatory variation was more common for both steady-state and stress-responsive expression differences, some examples of trans-regulatory variation were observed. The results provided may be useful to develop predictive models for gene expression responses. The RNAseq data is available at NCBI under PRJNA244661. Philipp Weckwerth, 2017

Data Available:

3/2017 Jason Wallace
Hirsch, CN et al. 2016. Plant Cell 28:2700-2714
   Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

Download the assembly here:

Sequence data from this article can be found in the Sequence Read Archive at the National Center for Biotechnology Information under accession number PRJNA258455. The PH207 genome multifasta file, GFF annotation file, transcript multifasta file, and protein multifasta file are available for download from the Dryad Digital Repository (DOI: 10.5061/dryad.8vj84). Additionally, the PH207 genome assembly results as Integrative Genomics Viewer (Broad Institute) tracks are available for public access at

It is well known that the maize B73 reference genome captures only part of the total diversity in the maize pan-genome. Hirsch et al. describe the sequencing and assembly of PH207, an elite inbred line from the Iodent heterotic pool. Multiple comparisons show that the PH207 assembly is of similar quality to the existing B73 genome, and comparisons between them show large amounts of structural variation between the two. Over 2500 genes were absent in one genome relative to the other ("presence-absence variants", or PAVs), and 136 gene families showed large amounts of expansion or contraction on one line relative to the other. PAVs were enriched in the pericentromeric regions, showed lower overall expression and more tissue-specific expression, and were enriched for functions related to stress responses. The two subgenomes from maize's ancient tetraploidization also showed extensive differential fractionation between the two lines. The large amount of genetic and transcriptomic differences between B73 and PH207 supports the idea that heterosis between maize lines may be driven by these line-specific variations. Comparison between these genomes highlights the importance of having multiple representative genomes for a species; additional maize genomes will doubtless be similarly useful in analyzing the variation present across maize germ plasm. Jason Wallace, 2017

3/2017 Fang Bai
Kelliher, T, et al. 2017. Nature. 542:105-109
   MATRILINEAL, a sperm-specific phospholipase, triggers maize haploid induction

Doubled haploid breeding is one of the most efficient ways to shorten breeding time and improve the crop uniformity. To study the developmental genetics underlying the haploid induction in maize, Kelliher et al. (2017) generated BC1 mapping populations by cross the Stock 6 derivative RWK to the inbred NP2460 and NP2391, and then backcrossed to the RWK. Combined with the fine mapping and sequencing data of the candidate genes, they found that a loss-of-function mutation in GRMZM2G471240 is responsible for the haploid induction. MATRILINEAL (MTL) encodes a patatin-like phospholipase and specifically locates in the cytoplasm of the male gametes. The novel edits in MTL lead to a 6.7% haploid induction rate. This discovery may lead to the in vivo haploid induction in economic crop breeding in the near future. Fang Bai, 2017

3/2017 Ruben Rellan-Alvarez
Romero-Navarro, JA et al. 2017. Nature Genetics 49:476-480
   A study of allelic diversity underlying flowering-time adaptation in maize landraces

There are currently no comments for this article.

3/2017 Lin Li
Kong, FY et al. 2017. Molecular Plant 10:516-519
   Regulation of leaf angle by auricle development in maize

Plant architecture is one of most important agronomic traits associated with grain yield in maize. The leaf angle is one of the major components of plant architecture, that affects plant density in the field, while the auricle, a hinge linking the leaf blade to the vertical stem, may affect leaf angle. However, the molecular association between auricle and leaf angle has not been fully demonstrated. The authors measured leaf angle and different properties of auricle across 102 diverse maize inbreds, and conducted RNA-Seq on auricles at early, middle, and late developmental stages in both B73 and 986 at V3 stage. The morphogenesis analysis indicates that the leaf auricle has a crucial effect on LA in a large population of maize inbred lines, and the diversity of auricle development contributes to LA in maize. Meanwhile, the transcriptomic analyses show that genes associated with cell division and elongation might be involved in auricle development, which provides novel insight of the molecular mechanisms determining LA and plant architecture in maize. Lin Li, 2017

This letter to the Editor contains information on RNA-seq and more genes, but lacks primary data and reference to data repository.

2/2017 Fang Bai
Xu, GH, et al. 2017. New Phytol. 0:doi: 10.1111/nph.14400
   Complex genetic architecture underlies maize tassel domestication

Maize has two types of inflorescences: the male inflorescence of tassel and the female inflorescence of ear. The architecture of the tassel is important for improving the crop yield and studying the maize domestication. In this paper, Xu et al. (2017) perform high resolution of quantitative trait loci (QTL) mapping on five tassel traits in the maize-teosinte BC2S3 population and identified 11 loci for tassel length,17 for tassel branch length, 12 for tassel peduncle length, 14 for tassel branch number, and 18 for tassel branch angle. They also found many known inflorescence architecture genes are in their QTL mapping region which indicate gene roles in tassel evolution and maize domestication. In addition, Xu et al. found that several known flowering time genes are also in the tassel QTL region and those flowering time genes might be involved in the natural variation during the tassel evolution. Fang Bai, 2017

2/2017 Jason Wallace
Jamann, TM; Sood, S; Wisser, RJ; Holland, JB. 2017. PLoS One. 12:e0168910
   High-throughput resequencing of maize landraces at genomic regions associated with flowering time

Whole-genome sequencing provides a wealth of data but can be overkill for researchers interested in only specific genetic regions. Jamann et al. describe the development of a multiplex PCR Ampliseq procedure to amplify and sequence a total of 72 kb across 20 genes related to maize flowering time (including vgt1, ZmCCT, and other high-confidence candidate genes). The authors used a total of 319 primer pairs multiplexed in two PCR reactions to amplify these regions across three maize inbreds, two hybrids, and 19 landraces; amplicons were then sequenced using IonTorrent technology. After tuning their SNP-calling pipeline, they had high sensitivity for calling reliable genotypes, including heterozygotes, and used them to identify genetic relationships among the maize samples. The authors estimate that one could use this method to interrogate 2-5 times as much genomic space and still maintain quality genotypes. Jason Wallace, 2017

Whole-genome sequencing provides a wealth of data but can be overkill for researchers interested in only specific genetic regions. Jamann et al. describe the development of a multiplex PCR Ampliseq procedure to amplify and sequence a total of 72 kb across 20 genes related to maize flowering time (including vgt1, ZmCCT, and other high-confidence candidate genes). The authors used a total of 319 primer pairs multiplexed in two PCR reactions to amplify these regions across three maize inbreds, two hybrids, and 19 landraces; amplicons were then sequenced using IonTorrent technology. After tuning their SNP-calling pipeline, they had high sensitivity for calling reliable genotypes, including heterozygotes, and used them to identify genetic relationships among the maize samples. The authors estimate that one could use this method to interrogate 2-5 times as much genomic space and still maintain quality genotypes. Jason Wallace, 2017

Gene Models from this paper: GRMZM2G154580, GRMZM2G011357, GRMZM2G180190, GRMZM2G095598, GRMZM2G033962, GRMZM2G031432, GRMZM2G031432, GRMZM2G031432, GRMZM2G031432, GRMZM2G045275, GRMZM2G067921, GRMZM2G179264, GRMZM2G700665, GRMZM2G405368, GRMZM2G085218, GRMZM2G038783, GRMZM2G359322, GRMZM2G092174, GRMZM2G381691

NCBI Sequence Read Archive SRA504653 (raw sequence read data):

2/2017 Philipp Weckwerth
Wang, Y et al. 2016. Frontiers Plant Sci 7:1654
   The Mechanisms of Maize Resistance to Fusarium verticillioides by Comprehensive Analysis of RNA-seq Data

The authors are reporting on RNA-seq data acquired from Kernels treated with Fusarium verticillioides of a highly resistant maize variety (BT-1). F. verticillioides is one of the most commonly reported fungal species responsible for ear rot in maize, which also leads to substantial accumulations of mycotoxins. By performing RNA-seq on F. verticillioides treated kernels the authors show that the resistance of BT-1 is due to induced transcription of genes associated with pathogen recognition and sub sequential responses, e.g. enhanced formation of secondary cell wall. Differential gene expression in susceptible (N6) and resistant (BT-1) maize varieties was confirmed by qRT-PCR and microarray. Interestingly, some of the genes strongly induced by F. verticillioides in the resistant variety BT-1 are associated with QTLs of ear rot resistance identified in previous studies, opening up the field to promote the identification of genes involved in ear rot resistance. The authors state in the paper that the RNA -seq data is submitted to NCBI, and is now accessible here: Philipp R Weckwerth, 2017

1/2017 Fang Bai
Gontarek, BC; Neelakandan, AK; Wu, H; Becraft, P. 2016. Plant Cell. 0:doi: 10.1105/tpc.16.00609
   NKD transcription factors are central regulators of maize endosperm development

During the seed growth, the endosperm supplies nutrients and signals to promote embryo development and seed germination. NAKED ENDOSPERM1 (NKD1) and NKD2 are duplicate genes which are INDETERMINATE DOMAIN (IDD) transcription factors important for maize endosperm development. In this paper, Gontarek et al. (2016) study the function of NKD1 and NKD2. Through the RNAseq experiment from endosperm of nkd1nkd2 mutant compared to the wild type, they found that NKD 1 and NKD2 regulate genes involved in a broad biological processes, such as hormone regulation, cell division and differentiation, starch accumulation and seed maturation, etc.. The authors performed Selection and amplification binding (SAAB) and Electrophoretic mobility shift assays (EMSAs) to identify 8-bp binding sequence (BCS) of [TA]-T-[TCG]-G-T-[CGA]-G-T for NKD1 and 6bp BCS of T-G-T-[CT]-G-[TG] for NKD2. Furthermore, they analyze the direct target genes of NKD1 and NKD2. Through a series of experiment, they showed that NKD1 and NKD2 work as homodimer and heterodimer mediated by the ID domain. Fang Bai, 2017.

1/2017 Jason Wallace
Yendrek, CR, et al. 2017. Plant Physiol. 173:614-626
   High-throughput phenotyping of maize leaf physiology and biochemistry using hyperspectral reflectance

There is a big push to develop rapid, high-throughput methods to phenotype traits in the field. Although there is much hype and expectation about different methods, in many cases it's unknown how well they will work in practice. Yendrek et al. Provide an analysis of hyperspectral reflectance data taken across a maize field under both normal and high-ozone (stressful) conditions. The data were collected by hand, which while not as high-throughput as a tractor- or drone-mounted system was still many times faster than the wet-lab sampling used to get the ground-truth data. Partial least-squares regression on the spectra were able to predict 5 out of 7 tested traits with good accuracy: chlorophyll content, nitrogen content, specific leaf area, photosynthesis rate, and sucrose. The two poorly predicted phenotypes were PEP carboxylation and oxygen radical absorbance capacity. Statistical analyses of the model-predicted phenotypes showed similar results to the true values, indicating that using hyperspectral imaging to monitor plants for these traits is could replace traditional wet-lab analysis, at least for routine use. Jason Wallace, 2017

1/2017 Ruben Rellan-Alvarez
Renny-Byfield, S et al. 2017. pp.10.1093/molbev/msx121 in Mol Biol Evol
   Gene fractionation and function in the ancient subgenomes of maize

After maize genome duplication many paralogous genes have been lost and many returned to single copy status of the subgenomes (maize1) has been less affected by fractionation than the other (maize2). It has been hypothesized that higher expressed paralogs should have a higher effect on the phenotype and therefore belong to the less fractioned subgenome. In this manuscript Renny-Byfield, Rodgers-Melnick & Ross-Ibarra use publicly available gene expression, phenotypic and epigenetic data test this hypothesis that higher expression genes. They found that maize1 paralogous genes explain more phenotypic variability ((measured as higher heritability) than their maize2 counterparts, that in general this corresponds with higher expression levels of maize1 paralogs and that this could be explained at least in part by higher levels of methylation in the maize2 subgenome genes. One unexpected result from their analysis is that maize1 singleton genes (lacking a paralogous copy) explain more phenotypic variability than maize2 genes even thought they have comparable expression levels. Ruben Rellan, 2017

1/2017 Philipp Weckwerth
Oliveira-Garcia, E; Deising, HB. 2016. Plant J 87:355-75
   Attenuation of PAMP-triggered immunity in maize requires down-regulation of the key β-1,6-glucan synthesis genes KRE5 and KRE6 in biotrophic hyphae of Colletotrichum graminicola

The authors functionally characterize KRE5 and KRE6, key enzymes in β-1,6-glucan synthesis, of the ascomycete Colletotrichum graminicola, a hemibiotroph that infects maize (Zea mays). After appressorial plant invasion, this fungus sequentially differentiates biotrophic and highly destructive necrotrophic hyphae. RNAi-mediated reduction of KRE5 and KRE6 transcript abundance causes appressoria to burst and swelling of necrotrophic hyphae, indicating that β-1,6-glucosidic bonds are essential in appressoria and necrotrophic hyphae. As RT-qPCR is not feasible due to unsynchronized differentiation of infection structures of C. graminicola, the authors used live cell imaging employing KRE5:mCherry and KRE6:mCherry knock-in strains and probing of infection structures with a YFP-conjugated β-1,6-glucan-binding protein. This revealed expression of these genes and exposure of β-1,6-glucan in conidia, appressoria and necrotrophic, but not in biotrophic hyphae. In contrast, overexpression of KRE5 and KRE6 in biotrophic hyphae leads to activation of broad-spectrum plant defense responses, including papilla and H2O2 formation, as well as transcriptional activation of several defense-related genes. The results suggest that down-regulation of synthesis and avoidance of exposure of branched β-1,3-b-1,6-glucan in biotrophic hyphae is required for attenuation of plant immune responses. Philipp Weckwerth, 2017

1/2017 Lin Li
Huang, XH. 2016. Nature. 537:629-633
   Genomic architecture of heterosis for yield traits in rice

Heterosis or hybrid vigor, usually refers to the phenomenon that hybrid offspring exhibit superior performance relative to that of their parents. Heterosis has been of immense economic value in agriculture, especially for the utilization in maize and rice. Despite extensive investigation, the molecular mechanism underlying heterosis remains elusive. It appears that there is not a single gene or mechanism but many genes or mechanisms associated with heterosis. In this study, the authors describes a comprehensive experiment, collecting ultra-high density of marker data and precise phenotypic data in 10,074 F2 lines from 17 representative hybrid rice crosses. Although this is still a QTL study, this study suggests that most heterozygous loci exhibit positive partial dominant effect, while a few loci with pseudo-overdominant or overdominant effect, contributing to the heterosis in hybrids. Most interestingly, a small number of genomic loci from female parents could explain a large proportion of heterosis. Such dominant parental effect has also been observed in the study in maize from Schnable group (Swanson-Wagner et al., 2009). This paper provides a clue to conduct heterosis dissection with the rapid progress of next generation sequencing and phenotyping in maize. Lin LI, 2017

12/2016 Yan He
Dong, XM, et al. 2016. Molecular Plant. 0:doi: 10.1016/j.molp.2016.10.007
   Dynamic and antagonistic allele-specific epigenetic modifications controlling the expression of imprinted genes in maize endosperm

Genomic imprinting, a classic epigenetic phenomenon, arises from allele-specific epigenetic modifications that are established during gametogenesis. The current knowledge have suggested that DNA methylation and H3K27me3 have plays critical roles in regulating genomic imprinting, however, little is known about how the contributions of allele-specific active histone modifications to imprinting in plant. In this study, the authors have identified 337 allele-specific H3K4me3 and H3K36me3 peaks in endosperm. The results showed that paternally expressed genes (PEGs) are mostly co-localized with paternally preferred H3K4me3 and H3K36me3, and vice versa, maternally expressed genes (MEGs) were usually associated with maternally preferred H3K4me3 an H3K36me3 peaks. Interestingly, the active H3K4me3, H3K36me3 and repressive H3K27 were present together in parts of PEGs. For constitutive PEG, H3K27 and H3K36me3 were specifically deposited on hypomethylated maternal alleles and hypermethylated paternal alleles. DNA methylation and H3K4me3 were specifically marked on paternal and maternal alleles around TSS of endosperm MEGs (endo-METs), respectively. In addition, a set of maternally expressed non-coding RNAs (MNCs) showed same allele-specific epigenetic features with endo-MEGs, indicated that a similar mechanism in regulating imprinted genes and non-coding RNAs. These results enhance the understating of the complex patterns depicting mutually exclusive epigenetic modifications associated with different alleles of imprinted genes which may have active roles for the development of maize endosperm. Yan He, 2016

12/2016 Arnaud Ronceret
Higgins, DM et al. 2016. Frontiers Plant Sci 7:1277
   The maize Divergent spindle-1 (dv1) gene encodes a kinesin-14A motor protein required for meiotic spindle pole organization

There are currently no comments for this article.

12/2016 Carolyn Rasmussen
Nannas, NJ; Higgins, DM; Dawe, RK. 2016. J Cell Sci. 129:4014-4024
   Anaphase asymmetry and dynamic repositioning of the division plane during maize meiosis

In this study, the authors describe a phenomenon observed during meiosis: metaphase and anaphase spindle asymmetry in the cell that is corrected by higher chromosome movement rates and longer distances. CFP-TUBULIN was used to label the microtubule structures while SYTO12, a live cell dye that binds nucleic acids, was used to label the chromosomes. The authors looked at chromosome movements during meiosis I, when homologous chromosome were separated, and meiosis II, when sister chromatids were separated and observed that chromosomes were pulled farther apart in meiosis II than meiosis I. When the spindle was asymmetrically localized in the cell, chromosomes moved further and faster to correct their location towards the center of the cell. The phragmoplast, the plant specific cytokinetic apparatus, was then formed in between the chromosomes rather than the original spindle position, suggesting that a specific interaction occurs between chromosomes (or the cell periphery) and the phragmoplast to establish its proper location. Although there is no mechanism yet known, this paper provides insight into the factors that help position chromosomes and microtubule structures in meiotic cells. Carolyn Rasmussen, 2016

12/2016 Michelle Facette
Mir, R et al. 2016. Plant Physiol 173:863-871
   DII-based auxin reporter in maize reveals low auxin signaling during telophase and early G1

There are currently no comments for this article.

12/2016 Eli Rodgers-Melnick
Svitashev, SK et al. 2016. Nature Communications 7: 13274
   Genome editing in maize directed by CRISPR-Cas9 ribonucleoprotein complexes

The recent successes of CRISPR/Cas9 genome editing in plants have generated a wave of excitement within commercial agriculture. However, the implementation of Cas9-delivered genome edits within product-driven breeding programs faces several challenges. In particular, off-target mutations must be minimized, both to avoid deleterious side-effects for the plant and to facilitate regulatory approval for the edited product. In a number of species, including several plants, delivery of a pre-loaded Cas9-gRNA ribonucleoprotein complex to the cell was shown to minimize off-target effects. However, previous RNP transformations in plants were limited to protoplasts, which rarely regenerate fertile plants among most crop species, including maize. In this study, authors Svitashev et al demonstrate the delivery of Cas9-gRNA RNPs to maize immature embryo cells through bombardment with a helium gene gun. The authors show that although the frequency and composition of the target-site mutations is similar between the RNP-based and DNA vector-based methods, off-target mutations at a known site for the DNA vector approach were nearly or completely eliminated under the RNP approach. Furthermore, the high efficiency of RNP-directed edits permits recovery of the 2-10% of plants containing edits in the absence of selectable markers. Thus, genomic editing of crop species may be achieved without the need for a selective media or the additional step of back crossing to eliminate off-target mutations. Eli Rodgers-Melnick, 2016

11/2016 Eli Rodgers-Melnick
Kadam, DC et al. 2016. G3 6:3443-3453
   Genomic prediction of single crosses in the early stages of a maize hybrid breeding pipeline

Modern maize breeding programs depend upon the optimization of single crosses between inbreds from different heterotic groups. Specific inbreds must move through several years of topcrosses to establish their general combining ability (GCA), while the latter stages of hybrid breeding program focus on discovering specific combinations of inbreds with high specific combining ability (SCA). Practically, only a small number of all possible hybrids can be tested across a program's target population of environments, so accurate prediction of single cross phenotypes is highly desirable. In this study, authors Kadam et al tested the use of single cross prediction for random sets of crosses between members of biparental families. Specifically, they made 6 biparental families from all combinations of 3 inbred lines in the Stiff Stalk Synthetic (SSS) and Non-stiff stalk (NSS) heterotic groups. They used two primary methods to estimate single-cross performance, comparing the older approach of using single cross covariance to that of using heterotic-group specific covariances to estimate GCA for all inbreds and SCA for all possible combinations. Generally, the authors find that the latter approach can lead to higher accuracy, particularly when neither inbred parent is present within the training set. Eli Rodgers-Melnick, 2016

11/2016 Yan He
Richter, A, et al. 2016. Plant Cell. 0:doi: 10.1105/tpc.15.00919
   Characterization of biosynthetic pathways for the production of the volatile homoterpenes DMNT and TMTT in Zea mays

Plant volatiles play important roles in defense against herbivores, fungi and bacteria, as well as in signaling interaction between plant and other organisms. However, it is not fully known about how the biosynthetic and the regulation pathway of every individual plant volatile in response to external stimuli. In this work, the authors utilized genome-wide association study (GWAS) in a nested association mapping panel (NAM) to exploit the natural variation of herbivore-induced volatiles. The results yield a set of quantitative trait loci (QTLs) controlling the variation in the production of volatile terpene. The most significant SNPs associating the emission of (E)-nerolidol, linalool, DMNT and TMTT fall into the promoter of the gene encoding the terpene synthase TPS2 (GRMZM2G046615). The biochemical experiments later demonstrate that TPS is responsible for the production of volatile mono-, sesqui-, and diterpene alcohols. Furthermore, the joint-linkage analysis identified two cytochrome P450 genes (GRMZM2G102079 and GRMZM2G139467) are capable of converting nerolidol into DMNT by oxidative degradation. In conclusion, the identified two monooxygenases and the associated DMNT biosynthetic pathway are distinct from those previously characterized DMNT and TMTTT synthsis in Arabidopsis, implying that the independent evolution of these enzymatic activities. Yan He, 2016

11/2016 Carolyn Rasmussen
Li, L et al. 2016. Sci. Rep. 6:34395
   Characterization of maize roothairless6 which encodes a D-type cellulose synthase and controls the switch from bulge formation to tip growth

In this paper, the authors identify roothairless6 (GRMZM2G432699) as a gene encoding a D-type cellulose synthase required for all root hair development in maize. The mutant was identified by a combination of bulked segregant RNA sequencing (BSR-Seq) and Seq-Walking. Seq-Walking uses Mutator (Mu) insertion sequences to identify the mutant locus. When the mutant is caused Mu insertion in the locus, the locus can be identified by amplifying all DNA segments flanking Mu transposon insertions from both the mutant and wild-type. These are then compared, and "mutant-specific" Mu insertions are identified. Those that were located in the mapping interval identified by BSR-Seq showed an insertion in GRMZM2G432699. Other mutant alleles confirmed the identity of the rth6 gene. rth6 mutants were able to initiate root hairs, but elongation was stalled. Not surprisingly, rth6 transcripts were most abundant in root hairs and roots when compared with other CSLD transcripts that do not play a role in root hair elongation. Finally, a model is proposed to discuss the potential role of RTH proteins in root hair elongation. RTH6, a cellulose synthase, likely extrudes cellulose at the tip to strengthen the shaft while RTH3, a COBRA-like protein organizes the cellulose and RTH2 generates hydroxyl radicals to loosen the cell-wall. Carolyn Rasmussen, 2016

11/2016 Arnaud Ronceret
Yang, CJ et al. 2016. Genetics 204:1573-1585
   A gene for genetic background in Zea mays: fine-mapping enhancer of teosinte branched1.2 to a YABBY class transcription factor

There are currently no comments for this article.

11/2016 Michelle Facette
Wang, G et al. 2012. Plant Cell DOI 10.1105/tpc.112.10136
   Opaque1 encodes a myosin XI motor protein that is required for endoplasmic reticulum motility and protein body formation in maize endosperm

There are currently no comments for this article.

10/2016 Yan He
Yao, DS, et al. 2016. PLoS Genetics. 12:e1006270
   Maize opaque10 encodes a cereal-specific protein that is essential for the proper distribution of zeins in endosperm protein bodies

Cereal storage protein are valuable nitrogen sources for human and livestock. Prolamins are the major storage proteins and deposited into protein bodies (PBs) that occur only in cereal gain endosperm. In this study, the authors used the strategy of the positional cloning to identify the gene underlying the Maize opaque10 (o10), a classic opaque endosperm mutant. The results showed that o10 encodes a novel cereal-specific PC protein. A detailed characterization of its functional domains revealed that its middle domain is responsible for its dimerization and its C-terminus is required for its ER localization and PB deposition, and its N-terminus is facilitating the formation of a ring-shaped layer in PBs through direct interaction with two major storage proteins (22-kD and 16-kD zeins). The loss-of-function of o10 caused the disruption in this ring-shaped distribution of 22-KD and 16-kDzeins, leading to the presence of misshapen PBs. These results demonstrated O10 protein is essential for PB morphology by regulating the ring-shaped distribution of 22-kD and 16-kD in maize endosperm. Yan He, 2016

10/2016 Arnaud Ronceret
Koo, DH; Zhao, H; Jiang, JM. 2016. Chromosome Res. 0:10.1007/s10577-016-9537-5
   Chromatin-associated transcripts of tandemly repetitive DNA sequences revealed by RNA-FISH

Tandemly repetitive DNA (satellite) are major component of heterochromatin. In maize, they are organized in long array in knobs, centromeric, pericentromeric and telomeric regions. This paper describes the detection of chromatin associated transcripts of four common of these satellite repeats by RNA-FISH. Bioinformatics analysis of the maize ESTs and mRNA seq database detect the presence of -low abundant or poorly recovered- transcripts associated with these satellites. RNAse treatment, competition with unlabeled probe and comparison with FISH signal confirmed the identification of the RNA signal in the nuclei. The 180bp knob repeats show transcripts associated with minor 180bp foci on interphase nuclei suggesting that they are transcribed from the small knobs loci. The RNA-FISH technique did not detect any transcript of the 350bp subtelomeric repeat. The telomeric (TTTAGGG)n show both sense and antisense RNA signal with more foci (10 to 15 per nucleoplasm) with probe detecting the (UUUAGGG)n containing RNA molecules than for (CCCUAAA)n (3 to 6 per nucleoplasm). This telomeric strand specific RNA-FISH pattern was also found in tobacco nuclei. The centromeric 156bp CentC repeat shows sense and antisense transcripts. RNAse treatment comparison analysis show that these structural heterochromatic RNA participate in the proper localization of nucleolar fibrillarin and the kinetochore protein MIS12 but does not affect the localization of CENH3. The paper suggests that an essential and functional component of heterochromatin could be based on structural RNA expressed from satellite. Arnaud Ronceret, 2016

10/2016 Carolyn Rasmussen
Lowe, KS et al. 2016. Plant Cell pp.10.1105/tpc.16.00124
   Morphogenic regulators baby boom and wuschel Improve monocot transformation

Overexpression of two embryogenic tissue promoting genes, Babyboom (Bbm) and Wuschel2 (Wus2), vastly increased transformation efficiency of maize lines that were previously difficult or impossible to transform. In addition, use of Bbm and Wus2 together allowed efficient transformation and eventual recovery of transformed plants from typically difficult starting materials including the embryos in mature seeds and seedling leaf tissue as well as transformation of sorghum, rice and sugar cane material. The Bbm and Wus2 cassette prevented successful regeneration so the authors cleverly designed removal of the Bbm and Wus2 cassette using Cre-lox mediated recombination controlled by a drought inducible promoter. The major drawback is that many of the plasmids used in this article contain selectable markers that may require multiple material transfer agreements. However, the probable utility of this cassette for transformation of more maize inbred lines and more flexible starting material will provide a major step forward for researchers working on maize or other monocots. Carolyn Rasmussen, 2016

Sequence data from this article can be found in the GenBank/EMBL databases under the following accession numbers: Zm-Bbm cDNA (CS155772); Zm-BBM protein (CAJ29869); Zm-Wus2 cDNA (EA275154); and Zm-WUS2 protein (ABW43772). The Os-Bbm gene can be found at OSA1 Release 7 (LOC_Os1g67410.1).

10/2016 Eli Rodgers-Melnick
Ko, DK, et al. 2016. PLoS Genetics. 12:e1006197
   Temporal shift of circadian-mediated gene expression and carbon fixation contributes to biomass heterosis in maize hybrids

In maize, approximately 10% of genes display oscillating expression patterns consistent with regulation by a circadian clock. Thus, any alterations to master regulators of circadian rhythms have the potential to promote major, systematic effects. Authors Dae Kwan Ko et al investigate the roles of the 2 maize homologs of CIRCADIAN CLOCK ASSOCIATED1 (CCA1), a master circadian regulator with associations to enhanced photosynthetic activity and biomass accumulation in Arabidopsis thaliana. The authors demonstrate a phase-shift in the binding of ZmCCA1 toward the morning hours in B73-Mo17 hybrids relative to inbreds, which is also associated with non-additive gene expression of the putative regulated genes during seedling developmental states. The amplified early induction of many genes - particularly those involved in carbon fixation - may have a direct role in producing the strong hybrid vigor forming the basis of modern commercial maize production. Eli Rodgers-Melnick, 2016

9/2016 Michelle Facette
Beydler, B et al. 2016. Plant Physiol 171:2648-2658
   The juvenile phase of maize sees upregulation of stress-response genes and is extended by exogenous jasmonic acid

There are currently no comments for this article.

9/2016 Andrea L. Eveland
Walley, JW, et al. 2016. Science. 353:814-818
   Integration of omic networks in a developmental atlas of maize

Walley et al have published a huge proteomic atlas of maize. This will be integrated with MaizeGDB and should be a wonderful resource for all of us. Andrea Eveland, 2016

9/2016 Arnaud Ronceret
McCaw, ME et al. 2016. Genetics 204:35-42
   Fast-flowering mini-maize: seed to seed in 60 days

This article presents two new inbred lines called Fast Flowering Mini-Maize (FFMM-A and FFMM-B) developed to have better characteristics for growing maize as an experimental model in greenhouse ie: reduced plants space requirements as well as a very short life cycle for maize. The FFMM lines are of particular interest for classroom and are a new toolkit for maize genomic research. The FFMMs flower in a month and produce viable kernels two months after plantation. These allow to have 5 to 6 generations of maize a year, characteristics that can compete with the other popular plant model Arabidopsis thaliana. These inbred were generated from four early flowering founders : Neuffer's Early ACR (University of Missouri; stock #60:8), Alexander's Early Early Synthetic (; stock #94-2-7 self), Tom Thumb Popcorn (Ames, IA; accession #PI 217412), and Gaspe Flint (Ames, IA; accession #PI 214279). Selection for earliest flowering, good seed production and general plant morphology during the 11 generations of inbreeding successfully improved the FFMM characteristics for a 'research model' compare to the founders. Karyotypes and genotyping by sequencing analysis determined the genomic ancestry and relative contribution of each founder for FFMM-A and FFMM-B. The two FFMM share 41% of their genome including a shared vegetative to generative transition1 (vgt1) variant (, coming from Gaspe Flint, associated with early flowering. As expected, the remaining genome structural differences due to different founder genomic contribution allowed heterotic effects when both lines are crossed. Interestingly, in contrast to a long believed correlation between genome size and life cycle length, the authors show that the genome size of FFMM-A is larger than B73 reference genome and that of FFMM-B. This result discredits the idea that a big genome size is a limitation for a short life cycle. FFMM-A genomic information is included as sample 'MM-1A' in Maize Hapmap3. Seed stocks of the two FFMM are available through the maize genetic stock center (FFMM-A stock TX40J;; FFMM-B stock TX40K; Arnaud Ronceret, 2016

9/2016 Carolyn Rasmussen
Giannoutsou, E; Apostolakos, P; Galatis, B. 2016. Planta. 0:10.1007/s00425-016-2574-7
   Spatio-temporal diversification of the cell wall matrix materials in the developing stomatal complexes of Zea mays

In this paper, the authors use antibodies against cell wall components to analyze changes in cell wall composition during stomatal development in maize. First, they define the developmental stages of stomatal development and then use specific antibodies against homogalacturonans with various levels of esterification, mixed-linkage glucans, rhamnogalacturonans and arabinogalactan proteins to determine when and where these cell wall components localize. Intriguingly, an antibody that recognizes calcium linked de-esterified or non-esterified homoglacturonans may potentially mark the location of the preprophase band, a microtubule and microfilament structure that determines the future division site in land plants. In addition, this antibody also highlights newly formed cell walls transiently during stomatal development. Arabinogalactans appear in young guard mother cells demonstrated using antibodies as well as a Yariv reagent dye. Rhamnogalacturonans recognized by the LM6 antibody decorated the walls of young guard mother cells and was observed at cell wall junctions. Overall, it is clear that molecular cues must work together with cell wall modifications to promote changes in cell shape and fate. While the specific roles of these cell wall modifications remain mysterious, this paper is an important step forward in understanding how development and cell wall modifications are integrated in maize. Carolyn G. Rasmussen, 2016

8/2016 Arnaud Ronceret
Dong, J et al. 2016. Proc Natl Acad Sci, USA 113:7949-7956
   Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads

There are currently no comments for this article.

8/2016 Yan He
Wu, L, et al. 2016. Sci. Rep.. 6:30641
   Comparative proteomic analysis of the shoot apical meristem in maize between a ZmCCT-associated near-isogenic line and its recurrent parent

ZmCCT, one of the critical genes regulating photoperiod response and its active expression under long-day conditions can postpone flowering in maize. However, till now, we know very little about the functional mechanisms of ZmCCT activity. In this research, the authors investigated the deferentially expressed protein in shoot apical meristem (SAM) between a near-isogenic line (NIL) and its recurrent parent using a proteomics approach, called the isobartic tags for relative and absolute quantification (iTRAQ). In sum, 386 protein were identified and fall into multiple functional categories, including energy production, photosynthesis, signal transduction, cell organization and cell biogenesis. These proteins serve as the candidate targets regulated by ZmCCT, and the involving pathways enhance our understanding about the mechanisms of ZmCCT in regulating the photoperiod in maize. Yan He, 2016

8/2016 Carolyn Rasmussen
Sebastian, J et al. 2016. Proc Natl Acad Sci, USA 113:8861-8866
   Grasses suppress shoot-borne roots to conserve water during drought

The authors showed that several Setaria species, several maize inbred lines and other members of the Poaceae family inhibit crown root formation under water deficit conditions. Under well-watered conditions S. viridis crown roots contribute significantly to root architecture. Addition of water locally near crown roots induced rapid new crown root growth indicating that crown roots are highly responsive to water. This response is matched by a significant transcript expression differences in the crown root region in well-watered and water deficit conditions including transcripts associated with oxidative stress and sexual reproduction. Use of a maize mutant in a lateral organ boundaries domain protein which does not produce crown roots, rootless concerning crown and seminal roots, had higher shoot and soil moisture under water deficit conditions likely due to a smaller root system. The authors showed that crown root growth inhibition shows significant variability in the maize nested association mapping lines to suggesting that this may be a trait that might be modified to improve crop yield under different local water conditions. The authors uploaded their expression data into the GEO database under accession GSE78054. RTCS = GRMZM2G092542. Carolyn G. Rasmussen, 2016

8/2016 Michelle Facette
Berny, MC et al. 2016. Molecular Plant 9:986-1003
   Single mutations in the transmembrane domains of maize plasma membrane aquaporins affect the activity of the monomers within a heterotetramer

Plasma membrane intrinsic proteins (PIPs) are protein channels found in biological membranes that facilitate the transport of water and small proteins. In this paper, Berny et al. describe the stoichiometry of a heterotetramer water channel (aquaporin) and the amino acid residues required for their physical association. PIPs are subdivided into two phylogenetic groups: PIP1s and PIP2s. PIP2s are plasma membrane water channels that, through physical interactions, recruit PIP1s from the ER to the plasma membrane. Berny et al. use tagged versions of PIP1;2 and PIP2;5 to confirm that these proteins assemble as different combinations of homo- and hetero-dimers (which then associate to form homo- or hetero-tetramers). They use predictive modeling to identify residues within the transmembrane domains of PIP1;2 and PIP2;5 that may facilitate their physical interactions. Using functional assays in Xenopus oocytes, they found characterized mutations in PIP1;2 at these key residues. Since PIP1;2 does not act as a water channel when expressed alone, but does when co-expressed with PIP2;5, mutation variants were expressed both on their own and with PIP2;5 to determine their activity within home and hetero-tetramers. Additionally, they also assayed the localization of these channels in oocytes and/or maize epidermal cells. Several mutations in PIP1;2 inactivated the PIP2;5 water channel when co-expressed. Reciprocally, other mutations activated the PIP1;2 channel, promoting channel activity when PIP1;2 was expressed alone. Notably, one particular mutation activated the PIP1;2 channel when expressed alone, promoting plasma membrane (instead of ER) localization, but when co-expressed with it inhibited it's PIP2;5 activity, rather than synergistically increasing it as seen with wildtype versions. The mutational analyses here provide structural insights on the interactions between the multiple PIP isoforms, and how their assembly and localization confers water-channel activity in maize. Michelle Facette, 2016

8/2016 Eli Rodgers-Melnick
Beissinger, TM et al. 2016. Nature Plants 2:16084
   Recent demography drives changes in linked selection across the maize genome

The extant genetic diversity of a given species arises from the variation produced by mutation and recombination filtered through the interacting forces of selection and genetic drift. The dynamics of the interplay between drift and selection depend on the product of the effective population size (Ne) and the coefficient of selection (s). Thus, changes in the former over time can lead to altered patterns of genetic diversity across a species. In this study of maize and teosinte genetic diversity, authors Tim Beissinger et al use the maize HapMap2 and HapMap3 data to unravel the dynamics of how selection has differentially impacted variation in the subspecies. The authors begin by confirming that site frequency spectra significantly differ inside and outside of genes in both maize and teosinte, likely reflecting the differing impacts of selection. They then use a demographic model to estimate a split between maize and teosinte 15,000 generations ago, with an initial maize Ne 5% of the ancestral effective population size. This initial model of incorporates post-domestication exponential growth and ongoing bidirectional gene flow, resulting in a modern Ne of 370,000. However, alternative models indicate this number may be several orders of magnitude larger. Strikingly, the authors find no evidence for the widespread impact of hard sweeps, with no significant differences in the diversity surrounding missense vs. synonymous substitutions. However, the authors do find that two estimators of Ne*s, the average number of pairwise differences and the number of singletons, significantly differ in opposite directions surrounding genic regions. Specifically, pairwise diversity has a greater reduction surrounding genes in teosinte, while singleton diversity is more strongly reduced in maize. Given that extant singleton polymorphisms are more likely to have arisen during recent population expansions, these results suggest that historical purifying selection was stronger in teosinte, while the increased effective population size of modern maize leads to enhanced purifying selection against rare deleterious alleles. Eli Rodgers-Meinick, 2016

7/2016 Yan He
Baldauf, JA et al. 2016. Plant Physiol 171:1144-1155
   Nonsyntenic genes drive tissue-specific dynamics of differential, nonadditive and allelic expression patterns in maize hybrids

Heterosis, or hybrid vigor, depicts the superior performance of heterozygous F1-hybrid progeny relative to the average of their homozygous parental inbred lines or the better performing parent. As a cross-pollinating plant, the F1-progeny display an exceptional heterosis. However, the molecular mechanisms determining the presence of heterosis are largely unclear. In this research, the authors investigated the performance of heterosis in maize primary root tissue, and found that the heterosis is reflected by differential, nonadditive and allelic transcriptome patterns. The number of differentially expressed genes between two parents is significantly beyond the comparisons of parent relative to hybrid. In addition, none of genes showed differentially expressed between reciprocal hybrids. Moreover, a large number of genes showed the alterations in nonadditive and allelic expression ratios in the comparison of parents versus hybrid, and two reciprocal hybrids. More importantly, the nonsyntenic genes relative to sorghum genome were highly overrepresented among those differential, nonadditive and allelic expression patterns compared to syntenic genes. This study highlights the importance of nonsyntenic genes in shaping the transcriptome landscape of hybrids to establish heterosis in the early developmental stage in maize root tissues. Yan He, 2016

7/2016 Carolyn Rasmussen
Best, NB et al. 2016. Plant Physiol pp.DOI: 10.1104/pp.16.00399
   nana plant2 encodes a maize ortholog of the Arabidopsis brassinosteroid biosynthesis protein Dwarf1, identifying developmental interactions between brassinosteroids and gibberellins

The authors showed that nana plant2 (na2, GRMZM2G057000) encodes an enzyme required for ∆24-sterol reductase activity used in brassinosteroid biosynthesis. NA2 converts 24-methylenecholesterol to campesterol. The na2 mutants had upright leaves, short stature due to internode elongation failure as well as well as defects in flower development due to inappropriate pistil development in the tassel (tasselseed). na2 expression was ubiquitous, but particularly high in mRNA from the collar region (containing the ligule, auricle and intercalary meristem). A paralog na2-like gene (GRMZM2G455658) was poorly expressed and had frameshift mutations consistent the possibility that it encodes a pseudogene. Next the contributions of brassinosteroid (BA) and gibberellin (GA) were assessed via phenotypic characterization of combinations of mutants in BR and GA biosynthesis throughout maize development. Double mutants revealed that BR and GA function additively in plant growth, but have distinct functions in leaf angle, flower development and tillering. GA biosynthesis mutants form anthers in the ear, while BR biosynthesis mutants do not: double mutants still produce anthers in the ear indicating that this phenotype does not depend on BR synthesis. In contrast, tillering occurs in GA biosynthesis mutants, but it requires active BR biosynthesis. BR biosynthesis mutants produce tasselseeds, but double mutants do not, indicating that the tasselseed phenotype requires active GA synthesis. In addition to assessing double mutant phenotypes, exogenous GA was applied to BR biosynthesis mutants to clarify the contributions of GA and BR. Overall, the data presented demonstrate interactions between GA and BR that vary widely throughout maize development highlighting the importance of assessing mutant phenotype contributions across multiple organs and developmental stages. Carolyn G. Rasmussen, 2016

7/2016 Michelle Facette
Ray, S et al. 2016. Plant Physiol 171:694-706
   Turnabout is fair play: Herbivory-induced plant chitinases excreted in fall armyworm frass suppress herbivore defenses in maize

Plants have multiple defense systems to address the multiple insults to their systems, including the salicylic acid (SA) pathway that promotes defense against biotrophic pathogens, and the jasmonic acid (JA) pathway that promotes defense against necrotrophic pathogens and herbivores. Previous work from the Luthe group showed that frass (excrement) from the fall armyworm suppresses maize host defense against herbivory by upregulating SA and associated genes and downregulating JA, thereby promoting armyworm feeding and growth. In this work, they identify some of the frass proteins active in this hijacking of maize defense. Fractionation of frass proteins and subsequent protein revealed the presence of several chitinases (including the known defense protein PR4) correlated with activation of SA genes that promote fall armyworm herbivory. Applying frass specifically depleted of chitinases eliminated this effect. Applying recombinant chitinases (instead of frass) to the plant also promoted fall army worm growth. This demonstrates how the fall army worm has taken advantage of the maize plant's own defense system to promote its own feeding and growth. Michelle Facette, 2016

7/2016 Arnaud Ronceret
Huang, W; Du, Y; Zhao, X; Jin, W. 2016. BMC Plant Biology. 16:88
   B chromosome contains active genes and impacts the transcription of A chromosomes in maize (Zea mays L.)

The B chromosomes are additional dispensable chromosomes first reported in maize a century ago by Kuwada (1915). They usually don't affect plant growth. The work of Huang et al. used a leaf RNAseq transcriptome analysis of lines containing or not the B chromosome (B73, B73+1B, B73+6B). All the B-specific sequences are homologs of A chromosome but present few SNP or sequence distinctive features. Because it is difficult to distinguish if the sequences are coming from a B chromosome or a A homolog, they also compare an oat additional line containing a maize B chromosome (Starter without B and Starter +B). Their analysis show that there is very limited number of gene up-regulated (115) and even fewer genes down-regulated (15) in line containing B chromosome compared to line without B chromosome. The RNAseq analysis allowed to identify three B-specific LTR-containing expressed sequences. Two Gypsy elements: comp75688 (3250 bp in length), comp74447 (1,633 bp in length) and a Copia element: comp30393 (484 bp in length). qRT-PCR showed that comp75688 was expressed in a B-dosage dependent manner. Four B chromosome specific genes were also analyzed in detail (GRMZM2G013761B, GRMZM2G356718B, AF466202.2_FG007B and GRMZM2G356653B named after their closest A-chromosome homologs respectively located on chromosome 4, 1, 10 and 1). The B chromosome localization of these elements was confirmed by FISH experiments. These analysis suggest that the origin of the maize B chromosome is a mosaic of elements from different A chromosomes. Arnaud Ronceret, 2016

7/2016 Eli Rodgers-Melnick
Wang, B et al. 2016. Nat Commun. pp. doi: 10.1038/ncomms11708
   Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

In any study of a complex genome, the specification of the transcriptome is an essential first step in the characterization of molecular systems. However, our ability to define a complete transcriptome is limited by the accuracy of gene prediction, the limitations of sequencing technology, the sampling of tissues, and our expectations of what a transcriptome should contain. In this study of the reference line B73, authors Bo Wang et al used PacBio sequencing to identify 111,151 unique transcripts from 6 tissues (root, tassel, ear, embryo, endosperm, pollen). This dataset covers approximately 70% of the maize RefGen_v3 filtered gene set, with an average of 6.5 isoforms per gene - a substantial increase over the 2.8 isoforms per gene in the RefGen_v3 dataset. Moreover, the number of isoforms is associated with cytosine methylation properties of the splicing junctions. The size distribution of the PacBio dataset also trends toward longer isoforms than the RefGen_v3 FGS. The authors find tissue-specific patterns of alternative splicing, though intron retention is dominant in all but the endosperm. They also discover a number of lncRNAs with tissue-specific properties, and they show that the epigenetic properties of lncRNA genes is similar to that of expressed protein coding genes. Interestingly, the authors were also able to discover and validate the presence of several trans-splicing events, in which the transcripts of distinct genes were spliced together at known splice junctions. The PacBio dataset is available through NCBI SRA under SRP067440. Eli Rodgers-Melnick, 2016

6/2016 Andrea L. Eveland
Rodgers-Melnick, E; Vera, DL; Bass, HW; Buckler, E. 2016. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1525244113
   Open chromatin reveals the functional maize genome

In this study, Rodgers-Melnick et al. profiled genome-wide chromatin accessibility in maize by analyzing differential sensitivity to micrococcal nuclease (MNase) digestion followed by high-throughput sequencing (DNS-seq). Their approach took advantage of relative sensitivity of chromatin to heavy and light concentrations of MNase to resolve regions of nucleosome occupancy and open chromatin from maize shoot and root tissues. MNase hypersensitive sites (HS) were identified as having significant DNS to heavy and light concentrations of MNase and were associated with potential occupancy of transcription factors and other regulatory machinery. For example, these regions were clearly associated with active promoter regions just upstream of transcriptional start sites and could be used, in most cases, as robust indicators of gene expression. They also showed that MNase HS marked known QTL in nongenic regions of the genome and can be used to resolve locations of distal enhancers of gene expression, e.g. the enhancer of tb1. The authors also showed that open chromatin regions were strongly associated with DNA hypomethylation and recombination hotspots. By projecting GWAS hits onto the open chromatin maps, they found 2-fold SNP enrichment within 2 kb of MNase HS sites compared to the space outside of these regions. Remarkably, while HS regions accounted for less than 1% of the genome, they explained ~40% of the heritable phenotypic variation in maize. Interestingly, the authors also showed that MNase HS regions are also significantly associated with GC-biased gene conversion, a nonadaptive selective force with potential implications for maize genetic load as well as heterosis. Rodgers-Melnick et al. demonstrate the far-reaching applications of DNS-seq in maize for defining regions of the genome that contribute to quantitative trait variation, which has enormous impacts on genome-assisted breeding and crop improvement. Datasets from this publication are available via the NCBI SRA (accession no. SRA302258). Andrea Eveland, 2016

6/2016 Michelle Facette
Egger, RL; Walbot, V. 2016. Dev Biol doi: 10.1016/j.ydbio.2016.03.016
   A framework for evaluating developmental defects at the cellular level: An example from ten maize anther mutants using morphological and molecular data

Anther development includes a series of mitoses and cell fate specifications and followed by a transition to meioses that produce the male gamete (pollen). Eggers and Walbot use a series of analyses to characterize ten maize mutants defective in pre-meiotic, somatic development within the anther, and present a model for anther development. Mitotic divisions in the anther include periclinal divisions yielding new cell layers (and cell types) and anticlinal proliferative divisions. In each mutant, total number of anther cells and number of supernumerary cells arising from incorrect periclinal divisions was counted at different anther lengths (i.e., developmental stage). Using these data, the mutants were classified into three classes: two mutants had anticlinal proliferation defects but no periclinal division defects and no supernumerary cells; four mutants had periclinal division defects, resulting in additional cell layes and abnormal anther lobe cell numbers; and another 4 mutants periclinal division defects yet normal anther lobe cell numbers. Within each of these 3 classes, distinct mutant phenotypes (such as which cell layer ectopically divides or when it divides) were identified. Transcriptomic comparisons of 3 mutants (all of which fall in to the third class with periclinal division defects but normal anther numbers) vs their wild type siblings were performed. Although certain groups of genes were similarly altered in the three mutants, they each had a unique complement of down or upregulated genes. The framework presented here, most notably the careful spatio-temporal analysis of cell division, provides hypotheses for when each of these genes is acting during the coordinated process of the somatic phase of anther development. It will surely paly important future roles in understanding plant cell division and cell fate determination as well as understanding male germline development in maize. Michelle Facette, 2016

6/2016 Arnaud Ronceret
Wolfgruber, TK et al. 2016. Frontiers Plant Sci 7:308
   High quality maize centromere 10 sequence reveals evidence of frequent recombination events

There are currently no comments for this article.

6/2016 Yan He
Carolyn Rasmussen
Je, BI et al. 2016. Nature Genetics 48:785-791
   Signaling from maize organ primordia via FASCIATED EAR3 regulates stem cell proliferation and yield traits

Je et al. discovered that FASCIATED EAR3 leucine rich repeat receptor like kinase protein inhibits the proliferation of stem cells by responding to a CLAVATA3-like peptide (ZmFCP1) which is made in nearby differentiating cells. The fea3 mutant overproliferates cells in the shoot apical meristem, tassel and ear meristems which leads to a fasciated ear and thick tassel phenotype but little overall growth defect. Je et al. showed that FEA3 localizes in the central region of meristems, and then searched for the putative ligand of FEA3. They identified a peptide ZmFCP1, which is a CLAVATA3 like peptide, that reduced wild-type but not fea3 mutant root or shoot apical meristem growth. Consistent with the hypothesis that ZmFCP1 is the FEA3 ligand, the Zmfcp1 mutant had large shoot apical meristems and fasciated ears and overexpression of ZmFCP1 led to a reduction in shoot apical meristem size. ZmFCP1 was not expressed in the shoot apical meristem, but instead in nearby cells and the leaf primordia. Interestingly, they demonstrate that this feedback loop is conserved also in dicots: Arabidopsis thaliana fea3 mutants were fasciated and had large shoot apical meristems and CLE27 was identified as the putative ligand. The authors show that weak fea3 alleles increased kernel number and ear weight in hybrids suggesting a potential use in crop improvement. Together, Je et al. identified a conserved feedback loop where the peptide ZmFCP1 expression originates in organ primordia to control nearby stem cell proliferation through the FEA3 receptor. Carolyn G. Rasmussen, 2016

Shoot apical meristems are stem cells occurring in niches, which balance proliferation with the incorporation of daughter cells into organ primordial. This balance is assured by a feedback signaling pathway including CLAVATA (CLV) and WUSCHEL (WUS). Although such feedback systems are well described in animals and plants, it is not known whether and how signals provide feedback signals from organ primordial to control the stem cell niches. In this study, the authors cloned the gene (GRMZM2G166524) underlying the maize FASCIATEM EAR3 (FEA3) mutant, and it encodes a leucine-rich-repeat receptor which functions in stem cell control and respond to CLE peptide expressed in organ primordial. The authors propose a model suggesting that this new CLE signal moves from the organ primordial to the SAM, where it is perceived by FEA3 to restrict stem cell proliferation. Yan He, 2016

6/2016 Eli Rodgers-Melnick
Bartlett, ME, et al. 2016. Molecular Biology and Evolution. 33:1486-501
   Evolutionary Dynamics of Floral Homeotic Transcription Factor Protein-Protein Interactions

The determination of floral organ identity is often used as the textbook example of developmental regulation in plants. Organ identity within the fluorescence is specified by the combinatorial action of MADS-box transcription factors acting according to the rules specified by the ABC(E) model of floral development. Petal and stamen development are directed by the B-class TFs, APETALA3 (AP3) and PISTILLATA (PI). Though obligate AP3/PI heterodimerization appeared early in angiosperm evolution, PI homodimerization has evolved independently several times in monocot and dicot lineages, indicating the protein-protein interactions of these critical TFs are relatively labile. In this study, authors Bartlett et al characterize the dimerization patterns of PI, the amino acid residues controlling PPI specificity, and their phenotypic effects of the PPI regimen on floral development in Arabidopsis thaliana. The grasses have two clades of the PI TFs - PI-1 and PI-2 - from an ancestral duplication. While most TFs in the PI-2 clade have the capacity for homodimerization, the maize ortholog, STS1, exists as an obligate heterodimer with its AP3 counterpart, SI1. The authors use domain swaps and site-directed mutagenesis to pinpoint a glycine (G) to aspartic acid (D) substitution at position 81 of STS1 that is sufficient to recapitulate homodimerization. Interestingly, examination of the maize HapMap2 data showed that the G allele was fixed in all the maize lines, segregating in the teosintes, and absent in the single sequenced tripsacum. Thus, fixation of STS1 obligate heterodimerization appears to be concomitant with maize domestication. Moreover, several residues with evidence of positive selection within the PI-2 clade coincided with probable PPI interfaces, based on alignment with orthologous protein structures. Eli Rodgers-Melnick, 2016

5/2016 Eli Rodgers-Melnick
Orozco-Ramirez, Q et al. 2016. Heredity 116:477-484
   Maize diversity associated with social origin and environmental variation in Southern Mexico

While many studies of plant evolution focus on genetic differentiation with respect to environmental adaptation, patterns of population structure among domesticated species also reflect their cultural heritage. Yet, few researchers have analyzed the interplay of cultural and non-anthropogenic environmental forces on a local scale. In this study, Orozco-Ramirez and colleagues characterize genetic and morphological differentiation of maize landraces in neighboring municipalities of disparate ethnicities within Southern Mexico. Each muncipality contains both mid and low-elevation regions, allowing partitioning of variance between anthropogenic and non-anthropogenic features. Morphological traits have little structure across the region, although they are differentiated slightly more according to municipality than according to elevation. The effects of differentiation due to sociological forces becomes clearer after examination of genetic data. Estimates of genetic differentiation from both STUCTURE and AMOVA show significant differentiation between municipalities but not between elevations within municipalities. Furthermore, the differentiation of putative maize races receives little support from the genetic data. Thus, while the effect of elevation on population differentiation is well-supported species-wide, cultural forces can have an even stronger impact on gene-flow at local scales. Eli Rodgers-Melnick, 2016

5/2016 Arnaud Ronceret
Hu, HX, et al. 2016. Genetics. 202:1267-1276
   The genetic basis of haploid induction in maize identified with a novel genome-wide association method

Haploid induction (HI) is a method now widely used to initiate the production of double haploids allowing the production of inbred lines in 1-2 generations. The actual diverse haploid lines derives more or less indirectly from the original haploid inducer "stock 6" described by Ed Coe in 1959. The history of haploid inducers development is retraced in Supplemental File S1 and their pedigree tree and relationships in File S2 and Figure 1. In order to find the genetic basis of HI, the authors developed an elegant new GWAS method called conditional haplotype extension (CHE) taking into account that the cases (inducers lines) are related to each other because they shear a common ancestor. Using the CHE approach using the data of an Illumina Maize SNP 50k bead chip they detect a common segment of 1 Mb on chromosome 1 found in the 53 inducers analyzed but not in 1482 non inducers lines. This region correspond to a previously QTL required for HI (qhir) found in different analyses on Bin1.04. This region was refined into two closely linked genomic segments named qhir11 (0.54Mb) containing a previously fine mapped (223kb) QTL for HI and qhir12 (3.97Mb). qhir11 was not diagnostic for differentiating inducers from non inducers while qhir12 shows a complete correlation. The resequencing of the inducer line CAU5 compared to non inducers allowed to identify a list of variants in 44 genes of the qhir11 region (File S5). From this list, the authors identified three genes candidates, two encoding a DNA binding protein (ZM01G18090 / GRMZM2G137502, a Dof zinc finger protein and ZM01G18020 / GRMZM2G135834, an ortholog of AtDEK3) and one encoding an ortholog of the ACR4 receptor kinase (ZM01G18110 / GRMZM2G096682). Further functional characterization of these genes will be needed to know whether the corresponding variants found in CAU5 can trigger HI in maize. This new GWAS / CHE method promises to be of interest to characterize historical mutants already introgressed in different backgrounds. Arnaud Ronceret, 2016

5/2016 Andrea L. Eveland
Qiao, Z, et al. 2016. PLoS Genetics. 12:e1005991
   ZmMADS47 regulates zein gene transcription through interaction with opaque2

In this study, Qiao et al. characterized the interaction between OPAQUE2 (O2), a classic bZIP transcription factor (TF) that regulates zein protein biosynthesis in developing maize kernels, and a MADS box TF that has high sequence similarity to OsMADS47, which was thus named ZmMADS47 (ZmMADS47 = GRMZM2G059102 v3 coordinates = 1:17964695-17986258;GenBank: ACG34827.1). The protein-protein interaction between these two TFs was previously identified in a yeast-2-hybrid screen (Zhang et al., 2012). Here, the authors confirmed this interaction in vitro as well as in vivo by co-IP; the latter suggested ZmMADS47 and O2 exist in a complex of ~550 kD in maize kernels 15 Days After Pollination (DAP). In the endosperm of developing kernels, ZmMADS47 expression peaked at 15 DAP, while o2 expression was detected at 12 DAP and peaked at 20 DAP. To further characterize the function of ZmMADS47, RNAi lines were generated that knocked down its expression in maize. RNAseq-based transcript profiling of 15 DAP kernels between the RNAi knockdown lines and non-transgenic controls identified 1,071 differentially expressed genes, including those involved in "nutrient reservoir activity" such as a number of 19-kD and 22-kD α-zeins and the 50-kD γ-zein (data from RNA-seq experiment available from GEO: GSE70609). The authors used an EMSA assay to further show that ZmMADS47 binds directly to promoters of affects zein genes via a CATGT motif and that mutations in any one of the five bases of this core motif abolished binding ability. Interestingly, this motif is present in previously identified O2 binding motifs. Through a series of additional experiments, the authors described a model where ZmMADS47 cannot activate expression of zein genes on its own, but can enhance the activation of zein genes by O2. Previous ChIP-seq analyses for O2 (Li et al., 2015; RNAseq: GSE61830; ChIPseq data: GSE63991) indicated that not all O2 zein targets are co-bound and co-regulated by ZmMADS47 and that zeins targeted by O2 show various gene expression responses in the o2 mutant, suggesting there are additional transcriptional regulators of zeins that have yet to be discovered. Andrea Eveland, 2016

5/2016 Carolyn Rasmussen
Kelliher, T, et al. 2016. Frontiers Plant Sci. 0:doi: 10.3389/fpls.2016.00414
   Maternal haploids are preferentially induced by CENH3-tailswap transgenic complementation in maize

In this paper, the authors demonstrate that using an engineered histone specific for centromeres, CENH3, allows efficient production of doubled haploids. Doubled haploids make rapid homozygous lines that are useful for industry and research. The engineered lines perform a little less than half as well (3.6% at best) as other haploid inducing maize lines (8-15%). First, they isolated a mutant in the ZmCENH3 gene (GRMZM2G158526) from the uniform Mu collection and also used RNAi to knock down expression. Next, two CENH3 variants were added back to theZmCENH3 mutants: one with a fluorescent protein fused to the full length protein, and one that replaced the CENH3 N-terminal tail with the standard Histone H3 tail from GRMZM2G158526. The CENH3 variant with the H3 tail has been used in other organisms to promote doubled haploids. Unfortunately, the strongest haploid inducer lines, which contained the CENH3 with the H3 tail, had variable results in multiple crosses. This variability potentially reflects the mixed background and raises the possibility of genetic modifiers of haploid induction within the lines (which contained both W22 and NP2222). Overall, this paper provides insight into improving the efficiency of doubled haploid inducers in maize. Carolyn G. Rasmussen, 2016

5/2016 Yan He
Li, YX, et al. 2016. Plant J. 86:391-402
   Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population

Flowing time is one of the major traits during maize domestication to facilitate the broad adaption from tropic to subtropical areas across the world. ZmCCT and VGT1, two genes principally attribute to the adaption of the flowering time have been identified. However, the former studies have also shown that the genetic components regulating flowering time in maize are linking to more than 40 genes. To comprehensive dissect maize flowering time variant, the flowering time traits were examined in an extremely large multi-genetic population, including two NAM panels and a natural association panel. By combining linkage and association analysis, a total of 90 flowering time loci were identified, which are either common or unique in different population backgrounds. The GWAS analysis demonstrated that about one thousand SPNs associated with flowering time and most of these SNPs distributed around 220 genic regions. These candidate genes provide a large repertoire of targets for further functional studies to interpret the molecular mechanisms in regulating maize flowering time. Yan He, 2016

Lists out the China Nested Association (CN NAM) panel.

5/2016 Michelle Facette
Egger, RL; Walbot, V. 2016. Dev Biol doi: 10.1016/j.ydbio.2016.03.016
   A framework for evaluating developmental defects at the cellular level: An example from ten maize anther mutants using morphological and molecular data

Anther development includes a series of mitoses and cell fate specifications and followed by a transition to meioses that produce the male gamete (pollen). Eggers and Walbot use a series of analyses to characterize ten maize mutants defective in pre-meiotic, somatic development within the anther, and present a model for anther development. Mitotic divisions in the anther include periclinal divisions yielding new cell layers (and cell types) and anticlinal proliferative divisions. In each mutant, total number of anther cells and number of supernumerary cells arising from incorrect periclinal divisions was counted at different anther lengths (i.e., developmental stage). Using these data, the mutants were classified into three classes: two mutants had anticlinal proliferation defects but no periclinal division defects and no supernumerary cells; four mutants had periclinal division defects, resulting in additional cell layes and abnormal anther lobe cell numbers; and another 4 mutants periclinal division defects yet normal anther lobe cell numbers. Within each of these 3 classes, distinct mutant phenotypes (such as which cell layer ectopically divides or when it divides) were identified. Transcriptomic comparisons of 3 mutants (all of which fall in to the third class with periclinal division defects but normal anther numbers) vs their wild type siblings were performed. Although certain groups of genes were similarly altered in the three mutants, they each had a unique complement of down or upregulated genes. The framework presented here, most notably the careful spatio-temporal analysis of cell division, provides hypotheses for when each of these genes is acting during the coordinated process of the somatic phase of anther development. It will surely paly important future roles in understanding plant cell division and cell fate determination as well as understanding male germline development in maize. Michelle Facette, 2016

4/2016 Arnaud Ronceret
Sailer, C et al. 2016. Curr Microbiol 26:331-337
   Apomixis allows the transgenerational fixation of phenotypes in hybrid plants

In order to continue feeding the planet with a world population expected to reach 9 billion people by 2050, agriculture need a second green revolution. It has long been expected that introducing apomixis in crop plants could be a solution to this major agronomic issue. Apomixis allows plants to reproduce by seeds containing a clonal progeny. In theory, apomixis could allow to propagate the hybrid vigor (heterosis) because it can propagate the genotype. However empirically it was not proved that such a strategy could work because of potential interferences between the poorly understood processes of apomixis and heterosis and/or trans-generational epigenetic effects. The study of the group of Ueli Grossniklaus now shows for the first time that the use of an apomictic reproduction allows to propagate the benefits of heterosis. The plant model used is a similar natural apomictic hawkweed (Hieracium pilosella) that confused Gregor Mendel 150 years ago. The study elegantly check if 11 F1 hybrid selected to reproduce clonally keep 20 agronomic relevant vegetative and reproductive phenotypes using appropriate statistical tests. Only one apomictic line out of the 11 show instability. The maintenance of the heterotic effect is observed in 90% of the case (18 of the 20 traits examined) during 2 apomicitc generations. The 2 traits that show instability through generations (age at flowering and number of leaves at bolting) are traits related to flowering known to be largely epigenetically influenced. This study is a proof of concept that the old idea of using apomixis for hybrid propagation has sound grounds and could be applied in crops. This analysis is a green signal to invent apomictic strategies to revolutionize maize production in the years to come. Arnaud Ronceret, 2016

4/2016 Michelle Facette
Majeran, W et al. 2008. Molecular & Cellular Proteomics 7:1609-1638
   Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells

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3/2016 Andrea L. Eveland
Yang, H et al. 2016. Plant Cell pp.doi: 10.1105/tpc.15.00691
   Genome-wide mapping of targets of maize histone deacetylase HDA101 reveals its function and regulatory mechanism during seed development

In this study, Yang et al. explored the role of the maize histone deacetylase, HDA101, in kernel development. Histone deacetylases (HDACs) remove acetyl groups from lysine residues of acetylated histones, typically leading to tight, inaccessible chromatin structure. In maize, the HDAC HDA101 influences several aspects of development, including kernel size. Proper kernel development relies on differentiation of key endosperm cell types early in development (~4-6 DAP; Days After Pollination) including the endosperm transfer layer (BETL), which functions in nutrient uptake from maternal tissue to the endosperm. Overexpression (OX) of HDA101 leads to smaller kernels, which is due, at least in part, to defects in transfer cell development. The authors showed that a significant number of BETL marker genes were mis-expressed in hda101 OX mutants, both in expression level and in spatiotemporal pattern. In normal, B73 developing kernels, HDA101 protein begins to accumulate ~3DAP, however, in hda101 OX mutant kernels, protein accumulation is delayed until later stages of development where it accumulates at higher levels compared with normal kernels. To determine the genetic mechanisms of HDA101 during early kernel development, the authors mapped genome-wide occupancy of HDA101 using an HDA101-specific antibody. ChIP-seq was performed with two biological replicates using 4DAP kernels from normal B73 plants. The hda101 OX mutant line was used as a negative control. In total, ~10k peaks were identified as putative binding sites, including ~7.5k corresponding to protein-coding genes. BETL-specific genes were not among these putative targets, suggesting indirect regulation of these genes. Similar to what has been shown for mammalian HDACs, HDA101 primarily targets genes with high and intermediate expression levels and here, binding tends to be enriched in TSSs. This is surprising given that HDACs are generally considered repressors of gene expression. The authors also showed a global increase in histone acetylation at 4DAP resulting from loss of HDA101 protein in the hda101 OX lines. They further performed ChIP-seq for histone H4 lysine (H4K5ac) in normal B73 and hda101 OX kernels at 4DAP and showed hyper-acetylation at H4K5ac in ~1/3 of HDA101 direct targets in hda101 OX lines, but this did not seem to alter transcript levels. Interestingly, a small subset of inactive genes that are negatively regulated during kernel development was also targeted by HDA101. Loss of HDA101 binding led to hyper-acetylation and expression of these genes, suggesting a mechanism by which HDA101 controls endosperm differentiation. Co-IP experiments also showed that HDA101 interacts with members of various chromatin remodeling complexes and co-repressors. Taken together, this work highlights a role for chromatin-related mechanisms in regulation of kernel size. Andrea Eveland, 2016

3/2016 Michelle Facette
Johnston, R et al. 2015. New Phytol 205:306-315
   Ontogeny of the sheathing leaf base in maize (Zea mays)

Johnston et al. use several microscopic techniques to describe leaf initiation in maize. Their detailed descriptions of leaves as they emerge from the meristem confirms and clarifies fundamental differences between monocot and dicot leaf emergence, and using these data they form a model describing the patterning of the sheathing leaf base and parallel venation found in monocots. Firstly, they use computed tomography (CT) imaging of leaves as they emerge. Their 3D analyses show that new sheath margins (but not blade margins) overlap from outset in plastochron 3, sheathing the shoot apex from emergence. They follow their CT analysis by using PIN1a-YFP and DR5-RFP expressing plants as well as a PIN1 antibody to determine the pattern of auxin transport within leaf founder cells. Finally, they use in situ localization to determine the expression of genes known to be involved in auxin biosynthesis and leaf patterning. Specifically, they determined the expression domains of the auxin biosynthesis gene SPARSE INFLORESCENCE1 (SP1); AUXIN RESPONSE FACTOR3a (ARF3a); the HD-ZIP transcription factors ROLLED1 (RLD1) and PHABULOSA1 (PHB1); and maize orthologs of the A. thaliana organ boundary gene CUP-SHAPED COTELYDON (CUC). These in situ analyses together with the PIN1 and DR5 localization data illustrate that auxin maxima occurs around the circumference of the shoot apex (as opposed to a localized bump in dicots). These maxima then lead to provascular strands and eventually parallel venation. These detailed analyses provide a model for fundamental aspects of monocot leaf development. Michelle Facette, 2016

3/2016 Eli Rodgers-Melnick
Bousios, A et al. 2015. Genome Res 26:226-237
   A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response

Approximately 80% of the maize genome consists of transposable elements (TEs), many of which remain capable of active transposition. Therefore, the suppression of TE-mediated mutagenesis is a ubiquitous feature of the maize regulatory landscape. In this study, authors Bousios et al characterize the targeting of siRNAs to the Sirevirus LTR genus of retrotransposons, which together comprise approximately 20% of the maize genome. After identifying 13,833 full length Sirevirus TEs, the authors examine the mapping of leaf, tassel, and immature ear siRNA libraries to the B73 reference genome. Although 21-nt, 22-nt, and 24-nt siRNAs map to locations spanning the LTRs and internal (INT) domains of all Sirevirus families, the authors discover consistent siRNA hotspots corresponding to palindromic sequences within cis-regulatory regions of the LTRs. Despite the common hotspot characteristics, members of separate families largely lack shared siRNAs. The authors also demonstrate that transcripts including the palindromic regions can form hairpin RNAs, which may provide a basis for the generation of siRNAs from primary transcripts. Interestingly, the authors observe a mixed relationship between the age of the Sirevirus TEs and the numbers of siRNAs targeting them. Although an average negative relationship exists between TE age and siRNA targeting density, very old elements tend to be targeted as heavily as very young elements - with siRNAs clustered around intact palindromic hotspots. The evolutionary basis for the apparent conservation of these LTR palindromic sequences in very old TEs is currently unclear, but future investigation may shed considerable light on the evolutionary dynamics and regulatory mechanisms involved in TE control. Eli Rodgers 2016

3/2016 Yan He
Li, C-L; Shen, Y; Meeley, RB; McCarty, DR; Tan, BC. 2015. Plant J. 84:785-799
   Embryo defective 14 encodes a plastid-targeted cGTPase essential for embryogenesis in maize

Embryogenesis is a complex process involving coordinated expression of thousands of genes with diverse functions. The embryo defective 14 (emb14) mutants represent a unique class of mutants with defective embryogenesis but endosperm develops normally. In this study, the authors map-cloned a maize emb14 mutant by transposon tagging, and concluded that Emb14 gene encodes a circular permuted, YqeH class GTPase protein, which putatively function in 30S ribosome formation in plastids. The cytological analysis identified that loss of Emb14 function causes arrested embryogenesis at the early transition stages. Emb14 protein is localized in chloroplasts and has GTPase activity showed by in vitro assay. Emb14 is constitutively expressed and highly abundant in transition stage of embryogenesis. The disruption of Emb14 results in severe reduction in the accumulation of 16S rRNA and plastid. In sum, this study demonstrates that EMB14 mutant is caused by the mutation in a GTPase gene, which is shown to be essential for embryogenesis in maize. Yan He 2016

3/2016 Arnaud Ronceret
Feng, C, et al. 2016. Journal of Genetics and Genomics. 43:37-43
   Efficient targeted genome modification in maize using CRISPR/Cas9 system

Feng et al. describe the use of the targeted genome modification method of 'Clustered regularly interspaced short palindromic repeats' (CRISPR)/Cas9 system in maize. Considering the interest of this new technique for the maize genome manipulation (see the article of Zhu et al. 2015 reviewed by Eli Rodgers-Melnick in 2/2016) the authors address two essential issues for the use of this technology. First the efficiency of the system was analyzed by the effect of a construct whose single guide RNA (sgRNA) was designed to target the 8thexon of the zebra7 / lemon white1 (Zmzb7 = GRMZM2G027059/ ZM01G51760) gene, the unique ortholog of the Arabidopsis Chloroplast Biogenesis 6 (CLB6 = AT4G34350) gene. The authors found several deletions in the targeted site and rapidly recovered an expected albino plant due to the production of two mutated alleles leading to the loss of function of the Zmzb7 gene. The relatively high ratio of mutants obtained was rationalized by checking the efficiency of their construct on transformed maize protoplasts. By analyzing indels in the targeted loci from the protoplast genomic DNA the authors were confident they could use their construct for the transformation and regeneration of mutated calli and plants. Their second important contribution was to show that it is possible to mutate not only euchromatic loci but also genes located in maize centromeric and pericentromeric regions. Targeted mutations in 5 (Hsg3 = GRMZM2G332562 / ZM05G22190 and Hsg4 = GRMZM2G080129 /ZM05G22230 on chromosome 5, Hsg12 = GRMZM2G438243 / ZM02G19480, Hsg6 = GRMZM2G170586 / ZM02G19610 and Hsg7 = GRMZM2G099580 / ZM02G19660 on chromosome 2) of the 12 tested heterochromatic located loci were efficiently obtained. In addition the efficiency of the mutagenesis was independent of the expression of the targeted loci. The authors have also evaluated the specificity of their constructs and found no off-target mutations if the PAM (protospacer adjacent motif) had more than 3 different base pair. This analysis shows that the CRISPR/Cas9 targeted mutagenesis system is not only highly specific but is efficient in euchromatic and heterochromatic regions of maize. Arnaud Ronceret, 2016

The authors targets 12 genes located in maize centromeric or pericentromeric heterochromatin. The 5 successfully mutated gene are listed in the Ed Board member comment. The 6 unsuccessful target gene models were: GRMZM2G091313, GRMZM2G083935, GRMZM2G170577, GRMZM2G000411, GRMZM2G429781, GRMZM2G342426, and the single undetermined target was GRMZM2G135228

3/2016 Carolyn Rasmussen
Jamann, TM et al. 2016. Theor Appl Genet 129:591-602
   A remorin gene is implicated in quantitative disease resistance in maize

The authors fine map a quantitative disease resistance locus to a maize remorin ZmREM6.3 (GRMZM2G107774) and demonstrate that a Uniform Mu remorin mutants are more susceptible to Northern leaf blight fungal infection. This quantitative disease resistance locus, located on the short arm of chromosome one, provides resistance to two fungi: Northern leaf blight (Setosphaeria turcica) and common rust (Puccinia sorghi) as well as the bacterial pathogen Pantoea stewartii that causes Stewart���s wilt. The Northern leaf blight locus was narrowed to a 243 kb region containing several candidate genes. Combining mutant and expression analysis allowed them to identify remorin as a protein conferring disease resistance: mutants were more susceptible to northern leaf blight. Remorin proteins are plant specific phosphoproteins that localize to membrane microdomains and have characterized roles in symbiosis and viral movement. Together, the authors used a variety of tools to identify genes required for quantitative disease resistance locus and finally showed that remorin ZmREM6.3 plays a role in fungal disease resistance. Carolyn G. Rasmussen, 2016

2/2016 Yan He
Pan, QC et al. 2016. New Phytol 210:1083-1094
   Genome-wide recombination dynamics are associated with phenotypic variation in maize

Meiotic recombination is the most important source of genetic variations in higher eukaryotes. Recently the genome-wide distribution of recombination has been mapped in Arabidopsis, rice and maize through large-scale population study. The results show that recombination is not uniformly distributed along chromosomes, while generally higher in chromosomal arm and lower in centromeric/pericentromeric regions. At a relative fine-scale, some regions showing much higher frequency of recombination is designated as recombination hotspots and the mechanism or genomic features underlying the appearance of hotspot emerge to be elucidated. In this research, recombination events were extensively surveyed in 12 maize segregation populations using high-resolution distribution of SNPs makers. The results showed substantial variations in the recombination frequency and distribution along maize chromosomes, which is consistent to several previous studies. Meanwhile, 143 recombination hotspots were identified, which locates in both intragenic regions and intergenic regions. Interestingly, the overall count of intragenic recombination events maintain invariable in a given population, and therefore, the variation of recombination between different populations mainly attribute to intergenic recombination. More importantly, the study found that the significant associations between intergenic recombination and variation in gene expression level as well as agronomic traits, pointing out that the intragenic recombination plays a role in plant phenotypic diversity. All these results provide novel insight into the association of recombination with gene expression and phenotypic variation, which will greatly enhance our understanding of recombination in maize evolution. Yan He, 2016

2/2016 Andrea L. Eveland
Baute, J et al. 2016. Plant Physiol pp.doi: 10.1104/pp.15.01883
   Combined large-scale phenotyping and transcriptomics in maize reveals a robust growth regulatory network

In this study, Baute et al. performed an integrated analysis of in-depth phenotyping of 197 maize recombinant inbred lines (RILs) belonging to two different segregating populations, and their correlation with tissue-specific transcript profiles, to resolve gene expression signatures contributing to leaf biomass traits. This work extends the authors' previous analysis of a B73xH99 bi-parental mapping population to now incorporate a MAGIC (multiparent advanced generation intercross) 8-way RIL population. Ten parameters related to leaf size traits were measured in the 197 RILs including leaf length, width, area and weight, 5 measures of growth rate kinetics, and size of the cell division zone (DZ). In addition, fresh and dry weight was measured at the seedling stage. In general, correlations (PCC) between traits tended to be stronger in the MAGIC population, likely due to more phenotype variation. Positive correlations between DZ size and leaf size traits suggest that the number of dividing cells is potentially a key factor in determining final organ size. Therefore, the authors tested transcriptional differences between the 197 genotypes by performing RNA-seq on the proliferative DZ tissue. They determined linear transcript-phenotype correlations for each of the traits in both populations separately and for each trait, selected the top 1% most correlated and most anti-correlated genes. This resulted in 226 genes that were correlated or anti-correlated with at least one trait in both populations. Annotation of this gene set revealed that functional processes related to "regulation of transcription", "protein synthesis" and "cell wall synthesis and degradation" were highly enriched. Of the 56 transcription factors identified in this gene set, many were related to hormone regulation, leaf architecture and chromatin structure, and tended to be robustly correlated with leaf size. A number of the 226 genes had previously been implicated in leaf size and growth processes, however the majority had not and 48 genes were of unknown function. To narrow these candidates, the authors performed network analysis by integrating publically available expression resources for maize and protein-protein interaction data leveraged from Arabidopsis. A highly-connected growth regulatory network of 185 genes and 943 edges was established and revealed sub-networks of candidate genes co-expressed with known regulators of organ growth and final size. Results from this work provide a high-resolution resource of co-expressed candidate genes related to leaf size and growth rate, which can potentially be leveraged for increased biomass in crop improvement programs. Andrea Eveland, 2016

2/2016 Michelle Facette
Thatcher, SR et al. 2016. Plant Physiol 170:586-599
   Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

In this paper, Thatcher et al., use RNA-seq to systematically examine different splice isoforms in the B73 inbred line in different tissues and under well-watered and drought conditions. After filtering out low abundance transcripts or those that were not in multiple biological replicates, they identified more than forty-eight thousand novel transcripts. They used Principal Components Analysis to determine that (based on the % relative abundance of a splice isoform) different tissue types and developmental stages separated more clearly than did drought and well-watered conditions of the same tissue. They further analyzed the types of transcript isoforms. Interestingly, the proportion of isoform variations caused by intron donor/acceptor changes was stable across tissues, while exon skipping was rare in most tissues but occurred more commonly in developing ears. This demonstrating that certain splice variants are under developmental control. Using established rules from the literature, they also analyzed whether certain splicing isoforms would undergo relative increases or decreases in nonsense-mediated decay. While many isoforms resulted in a predicted increase or decrease in nonsense mediated decay, no particular tissue experienced more (or less) nonsense mediated decay than other tissues. They then proceeded to examine specific examples of changes in transcript isoform abundance, drawing examples from changes across embryo, endosperm vs seed development or well-watered vs drought conditions. This included a variety of examples such as those that result in different protein isoforms or those that result in alternate C-terminal untranslated tails, potentially resulting in differences in nonsense mediated decay. They conclude the paper by showing that across different tissues, there was a positive correlation between the expression of splicing-associated genes and the number of genes undergoing alternative splicing, suggesting that expression of these splice factors contribute to alternative splicing, and that it is indeed a developmentally controlled process. They further give an example of a particular splicing factor whose expression correlates well across drought and well-watered conditions, hypothesizing that it may play a role in alterative splicing during drought. Together, the paper gathers a large amount of data of alternative splice isoforms in maize and lends evidence towards developmental and environmental splice-specific changes. Michelle Facette, 2016

2/2016 Eli Rodgers-Melnick
Zhu, JJ et al. 2016. Journal of Genetics and Genomics 43:25-36
   Efficiency and inheritance of targeted mutagenesis in maize using CRISPR-Cas9

Although the promise of target-specific genomic edits has been within the grasp of plant geneticists since the advent of zinc finger nucleases (ZFNs), the previous ZFN and TALEN procedures require laborious and expensive protein engineering. The introduction of the CRISPR/Cas9 system has since enabled high-throughput, inexpensive edits to many species through the use of highly-configurable guide-RNAs (sgRNAs) for target sequence search. Previously published work on CRISPR/Cas9 editing in maize studied mutagenesis in stable T0 lines and following transient somatic cell transformation. In this study by authors Zhu et al, transformation efficiency, off-target effects, inheritance, and impacts on the global transcriptome are studied following transformation of maize protoplast with an Agrobacterium tumefaciens-delivered sgRNA-Cas9 expression vector. The authors discover approximately 2.4 million unique genic sgRNA targets within the B73 genome, which encompass over 95% of high-confidence protein coding genes. Over half of these target stites are contained within the first 2 coding exons, enabling targeted knock-outs of most maize genes. They take advantage of the qualitative phenotype induced following knockout of the PSY1 gene to profile both mutational efficiency and inheritance of mutations into the T1 generation. Of the 7/52 T0 lines positive for the Cas9 protein, mutation frequencies differed due to variation in the developmental stage where edits occurred. Indeed, while the seedling from one line was uniformly heterozygous for single mutant versions of both alleles, the other six lines contained a variety of edits to the target regions with mutational efficiencies between 65% and 87%. These numbers and the associated variegated phenotypes indicate that Cas9 continues to catalyze directed double-strand breaks throughout development. Yet, examination of computationally-identified regions of similarity to the targeted PSY1 region yielded no evidence of off-target effects. Moreover, self-fertilization and crosses to wild-type plants yielded the expected Mendelian inheritance patterns within kernels, with the corresponding seedling phenotypes, indicating that CRISPR/Cas9 edits are stably inherited by the T1 generation. Lastly, the lack of any significant expressional changes to the mutant transcriptome further substantiates the use of CRISPR/Cas9 for precise genetic experimentation in the highly complex and repeat-rich maize genome. Eli Rodgers-Melnick, 2016

2/2016 Carolyn Rasmussen
Lunardon, A; Forestan, C; Farinati, S; Axtell, MJ; Varotto, S. 2015. Plant Physiol. 0:DOI: 10.1104/pp.15.01205
   Genome-wide characterization of maize small RNA loci and their regulation in the required to maintain repression6-1 (rmr6-1) mutant and long-term abiotic stresses

The authors performed small RNA (sRNA) sequencing under well watered, drought and salinity conditions to identify differentially expressed sRNAs. Surprisingly few sRNAs were differentially expressed under drought and/or salinity conditions. To identify specific 24-nucleotide small interfering RNAs amplified by RNA polymerase IV, the authors compared small RNA generated in wild-type and a mutant in a subunit of RNA polymerase IV, the required to maintain repression 6 (rmr6) mutant. After sequencing small RNAs, they identified 48 MIRNA loci and ~250,000 non-MIRNA loci. New MIRNA loci, characterized by RMR6 independent accumulation of 21 and 22 nucleotide miRNAs, were identified: 3 from the miR166 family and 6 previously uncharacterized miRNA families. Several miRNAs were altered upon abiotic stress conditions: miR156 was induced by drought, while the phosphate homeostasis regulator miR399 was down regulated. Very few sRNA loci were altered, but five trans-acting short interfering TAS3 loci were down-regulated in drought-stressed plants, similar to previous observations. In general, differentially expressed genes under various conditions were not due to the loss of 24 nucleotide siRNAs in the rmr6 mutant, suggesting that siRNAs are not immediately necessary to maintain heterochromatic regions of the DNA. Carolyn G. Rasmussen, 2016

2/2016 Arnaud Ronceret
Oury, V et al. 2015. Plant Physiol pp.doi: 10.1104/pp.15.00268
   Ovary apical abortion under water deficit is caused by changes in sequential development of ovaries and in silk growth rate in maize

What is the effect of drought on ear seed-set in maize ? The cause of the typical ear devoid of fertilized kernel at its apex is now explained by extensive morpho-physiological analysis by Oury et al.. In water deficit conditions at the time of anthesis, grain abortion is observed, even when viable pollen is used for pollination. The authors followed for almost a month ovary volume and silk growth as a function of time and position on the ear in four hybrids under four levels of water deficit. The authors found that in water deficit conditions, silk growth rate decreased and stopped simultaneously for all ovary cohorts 2 to 3 days after first silk emergence, 5 days earlier than in well-watered plants. Abortion occurred in the youngest ovaries whose silks did not emerge 2 days before silk arrest. This mechanism allows production of at least few viable seeds under water deficit, but causes major yield loss. Its modelling may have important consequences for breeding drought tolerant maize. Arnaud Ronceret, 2016

1/2016 Andrea L. Eveland
Mejia-Guerra, MK, et al. 2015. Plant Cell. 0:doi: 10.1105/tpc.15.00630
   Core promoter plasticity between maize tissues and genotypes contrasts with predominance of sharp transcription initiation sites

In this study, the authors present genome-wide maps of transcription start sites (TSSs) in maize using CAGE (cap analysis of gene expression). Their analyses, which included genotype- and tissue-specific TSS profiles, can be used to determine the location of core promoters in the maize genome and variation in promoter architecture contributing to cis-regulatory differences in gene expression. Each gene is typically characterized by multiple TSSs, which collectively make up a promoter cluster. Results from this study showed that the majority of maize promoter clusters display a sharp peak (in plots of TSS vs. genome position), similar to those in mice, yet different from Drosophila and Arabidopsis, where promoter clusters are predominantly broad. The authors speculate that this potential link between core promoter shape and genome size may reflect a mechanism for more focused transcriptional initiation in species with large, repetitive genomes, such as maize and mouse. In addition, a link between promoter shape and gene expression (both level and tissue-specificity) was observed based on publically available maize RNA-seq data. In general, genes associated with broad promoter clusters showed higher median expression levels than those with sharp promoters, however the most highly expressed genes tended to have sharp promoters. Approximately 38% of all maize genes harbor a TATA motif, which is enriched in sharp promoters. Other specific DNA motifs were also preferentially enriched in promoter clusters with either broad or sharp shapes. Comparative analysis of CAGE profiles between two tissues, roots and shoots of 14 day old seedlings, and from two divergent maize inbred lines, B73 and Mo17, revealed hundreds of instances of tissue- and haplotype-specific TSS occurrences. For 11 genes, shifts in the dominant TSS between B73 and Mo17 resulted in a new ATG. For most of these genes, indels were identified, suggesting genetic variation can generate alternative TSS. The authors chose a subset of genes with predicted alternate promoter usage and experimentally validated that they indeed generated diversity in protein size and localization. This study represents the first experimentally generated, genome-wide analysis of transcription initiation in maize. Results from this work provide a valuable resource for dissecting cis-regulatory architecture and gene regulation in maize, which will be critical as we move towards precision breeding and engineering for crop improvement. This resource also significantly improves annotation of the maize genome. Andrea Eveland, 2016

1/2016 Michelle Facette
Vilela, B et al. 2015. Molecular Plant 8:709-721
   Casein kinase 2 negatively regulates abscisic acid-activated SnRK2s in the core abscisic acid-signaling module

Vilela et al. describe the phosphoregulation of the maize Snf-related kinase2 (SnRK2) ZmOST1. ZmOST1 orthologous to Arabidopsis OPEN STOMATA1, which is a key regulator of ABA signaling.OST1 kinase was previously thought to be regulated by autophosphorylation, but here the authors use biochemistry to demonstrate that Casein Kinase 2 (CK2) phosphorylates and regulates the stability of maize OST1, thereby adding another regulator to the ABA signaling module. Using in vitro kinase assays, they show that CK2 phosphorylates ZmOST1 within the "ABA-box" located in the C-terminus of the protein. Using transient assays in tobacco, they show that ZmOST1 normally accumulates in the nucleus cytosol, but when CK2 is co-expressed, OST1 localization shifts towards almost exclusive nuclear, and accumulates in nuclear speckles. Moreover, co-expression of OST1 and CK2 leads to eventual OST1 degradation, and this degradation is inhibited by the addition of MG132, implicating proteasome-degradation. This degradation is also dependent on the ABA-box. Moreover, phosphomimic mutations in OST1 at the site of CK2 phosphorylation increases the interaction with the PP2C ABI2, another core module of ABA receptor. Finally, transgenic maize lines overexpressing wildtype OST1 are hypersensitive to ABA; and transgenic lines overexpressing a phosphodead version of OST1 are even more hypersensitive to ABA. Together, the data suggest that CK2 phosphorylation negatively regulates ABA signaling by promoting proteasome-dependent degradation of OST1 kinase. This adds another key regulator to the ABA signaling pathway. Michelle Facette, 2016

1/2016 Eli Rodgers-Melnick
Leiboff, S et al. 2015. Nature Communications 6: 8974
   Genetic control of morphometric diversity in the maize shoot apical meristem

The shoot apical meristem (SAM) harbors the pool of stem cells that ultimately give rise to all the aboveground organs in plants. Accordingly, the SAM has been the target of numerous small-scale genetic studies in a variety of model species. However, despite elucidating the detailed genetic network underlying SAM development, mutational approaches do not necessarily illuminate the naturally-occurring genetic variation associated with differences in SAM morphology. In this study, Samuel Leiboff and colleagues characterize the morphology of the SAM in 369 diverse maize inbred lines using a simple parabolic model. They first demonstrate the predictive potential of microscopic SAM morphology by quantifying its correlation with adult quantitative traits, including flowering time, plant height, and stem diameter. The core of the study is then devoted to mapping the basis of natural SAM morphological differences using mixed model GWAS. Like many studies of traits putatively under high purifying selection, GWAS did not uncover any previously identified master regulators of SAM development. Nonetheless, the authors do identify 23 candidate genes, including genes with putative functions in hormone transport and cell division. They further functionally characterize the microscale physiological effects associated with alternative forms of associated SNPs. For instance, in situ transcript hybyridization demonstrates that a non synonymous mutation in the third exon of ZmLAX2, a predicted regulator of auxin influx, is associated with extension of its expressional domain into the SAM flank across from the incipient P0 leaf primordia. SNPs from two other candidate genes, ZmSDA1 and ZmBAK1, were found to be associated with increases in cell number and cell size, respectively, independent of variation in SAM volume. As the era of high-throughput phenomics and genomic prediction ramps up, the genetic dissection of seedling microscale traits and their relationships to yield components in adult tissues will likely rise to greater prominence. Time will tell whether such such microscopic variation will inform future crop growth models and methods for genomic prediction. Eli Rodgers-Melnick, 2016

1/2016 Arnaud Ronceret
Li, X et al. 2015. Nature Communications. pp.doi: 10.1038/ncomms7648
   Dissecting meiotic recombination based on tetrad analysis by single-microspore sequencing in maize

Analyzing meiotic recombination is of fundamental importance for understanding the dynamic of evolution of intraspecific genome diversity. Li et al. adapted for the first time in maize the classical toolkit of meiotic recombination studies using tetrad analysis. The sites of recombination can now be directly analyzed using high throughput sequencing of individual microspore coming from a single male meiosis. In order to trace recombination, two divergent genomes of the sequenced inbred parents Zheng58 and SK were used. The technique is based on micropipette isolation of male tetrads (the four microspores coming from a meiotic division) collected from immature meiotic tassels of two F1 (SK/Zheng58) plants. From an individual tetrad, each microspore containing an haploid recombined chromatid is isolated and analyzed at the whole genome sequence level thanks to single microspore genomic DNA amplification and sequencing by Illumina HiSeq. The sequencing of 96 chromatids from 24 tetrads lead to a high resolution mapping of 924 crossing overs (COs). The number of COs per male meiosis varies from 8 to 29 and seems distinct among the two individual plant analyzed. Most of the COs occurs in genes, and are mainly found in 5' and 3' UTR regions. The strength of interference was measured using coefficient of coincidence. Interestingly, it identifies a strong negative interference at the whole chromosome level, as in barley, but positive interference for COs closer to 10 Mb. In addition a weak chromatid interference phenomenon was also observed. This new technique open the possibilities to dissect in depth the recombination process in different hybrids, in different conditions as well as in meiotic mutants affecting recombination. It will be interesting to follow its more challenging development in female tetrad in order to understand at the whole genome level the distinct recombination rate and pattern of female meiosis. An associated detail protocol of this technique can be found at: Arnaud Ronceret, 2016

1/2016 Carolyn Rasmussen
Sidhu, GK, et al. 2015. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1514265112
   Recombination patterns in maize reveal limits to crossover homeostasis

The authors demonstrated that there is significant variability in the number of crossovers among different inbred lines, and further, that there is a strong correlation between amount of meiotic double strand breaks and crossing over events. This indicates that crossover homeostasis (where the number of crossover events is tightly regulated) is not the major driver of crossover number in maize. Double strain break number is strongly correlated with crossover number for both inbred lines and also for hybrids: the genetic distance between parents in hybrids did not increase the amount of crossovers. The minimum amount of crossing over, required for chromosome stability and increased genetic diversity, is one per homologous chromosome. The authors developed an elegant method combining chromosome spreading with three dimensional image reconstruction to assess the number of crossovers, which they used to measure crossing over events as well as chromosome pairing. One hypothesis based on data from non-plant organisms was that chromosome pairing and synapsis is associated with crossing-over, but this was not the case in maize: synaptonemal complex distances were similar in inbred lines with drastically different crossover number. A positive linear correlation was observed between double-strand breaks and crossing-over while a negative linear correlation was observed between crossover number and crossover interference. Overall, the authors propose that increasing the number of double strand breaks will lead to more recombination. Carolyn Rasmussen, 2016

1/2016 Yan He
Qi, W et al. 2015. Plant Physiol 170:971-988
   Maize reas1 mutant stimulates ribosome use efficiency and triggers distinct transcriptional and translational responses

As a fundamental cellular process, ribosome biogenesis plays key roles in nearly all cycles of plant development. However, the cellular responses to impaired 60S ribosome biogenesis are not fully understood. In this paper, the authors found that, the reduced 60S ribosome biogenesis in a mutant called rea1-ref/dek, caused seed-lethality in maize via differentially regulating the transcription and translation of a large number of genes which are involved in translation efficiency and cell proliferation. Rea1 encode an AAA-ATPase, an enzyme controlling 60S ribosome export from the nucleus to the cytoplasm after ribosome maturation. The authors identified that in dek mutant, mature 60S ribosome subunits are decreased in the nucleus and cytoplasm, whereas accompanied with increased proportion of actively translating polyribosomes in cytosol. In addition, the authors found that the general translation efficiency was increased since phosphorylation of eIF2alpha was reduced but the eEF1alpha level was increased. Moreover, there is selective translational regulation of different groups of genes for intensive usage of quantitatively limited mature ribosome. All the above mentioned abnormalities inhibited cell proliferation, leading to slower growth and survival of maize seed development. This study provides more insight into cellular responses after impaired ribosome biogenesis. Yan He, 2015

12/2015 Carolyn Rasmussen
Velez-Bermudez, IC et al. 2015. Plant Cell 27:3245-3259
   A MYB/ZML complex regulates wound-induced lignin genes in maize

Wounding causes lignin accumulation in plants. Lignin, formed from phenyl propanoid monomers that are assembled into higher order secondary structures, has an important function in increasing rigidity and hydrophobicity of the cell wall by binding polysaccharides. Here, the authors provide solid mechanistic evidence elucidating part of the pathway from wounding to lignin biosynthesis. First, they demonstrate that wounding or methyl-jasmonate treatment causes proteosome dependent degradation of two transcriptional repressors, MYB11 and ZML2, which in turn derepresses one of the lignin biosynthetic genes, caffeic acid O-methyl transferase (comt). MYB11 is a myeloblastosis (MYB) R2R3 type transcription factor that has an ethylene responsive element binding factor associated amphiphillic repression (EAR) domain. ZML2 is a TIFY type transcription factor whose gene expression pattern matches that of myb11. Since ZML homologs are both known to regulate wounding response and to interact with R2R3-MYB transcription factors, the authors tested their interaction. These two transcription factors physically interact with each other and their interaction requires the EAR domain of MYB11. The EAR domain is additionally required for MYB11 proteosome degradation. Both ZML2 and MYB11 bind in vivo to the comt promoter at the same time, determined by using serial chromatin immunoprecipitation (ChIP). The promoter binding sites, identified as AC-rich for MYB11 and GAT(A/C) for ZML2, in the comt promoter were 30 base pairs apart, and their model suggests that the two repressors not only bind the DNA, but also bend the DNA to bind to each other to repress comt gene expression. MYB11 and ZML2 bind promoter regions of several other lignin genes. ZML2 also interacts with two other closely related R2R3-MYB transcription factors, MYB31 and MYB42. Together, ZML2, MYB31 and MYB42 bind to the promoter of two lignin genes. The authors show that conserved cis-regulatory modules are found in several lignin genes across multiple species, suggesting a common regulatory module that controls coordinated lignin gene expression upon wounding. Carolyn G. Rasmussen, 2015

12/2015 Chung-Ju Wang
Li, Q, et al. 2015. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1514680112
   RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

In organisms with large genomes, like maize, genes are often surrounded by hundreds of kilobases of intergenic sequence that is comprised of transposons and tandem repeats. These repetitive sequences are associated with DNA methylation, specific histone modifications that confers repressive chromatin features, called heterochromatin. However, the majority of genes (85.5%) are positioned near heterochromatic transposons (within 1 kb) in the maize genome. How chromatin structures are regulated in order to maintain the heterochromatic state for repetitive sequences and the euchromatic state for active genes is still elusive. RNA-directed DNA methylation (RdDM) is the major mechanism of de novo cytosine methylation in all CG, CHG and CHH sequence contexts (where H can be A, C or T), and it is thought to play roles in suppression of transposons and genes. The RdDM pathway is particularly important for CHH methylation, since CG and CHG methylation are primarily maintained at high fidelity following DNA replication by separate pathways. Although many components of the RdDM machinery have been identified, the downstream effects of DNA methylation remain less clear. Previous research showed that, in maize, methylated CHH (mCHH) islands are often found near genes, whereas CG and CGH methylation are associated with transposons. In this study, Li et al. analyzed whole-genome bisulfite sequencing (WGBS) data and gene expression profiles of B73 seedlings and found elevated mCHH islands distributed in the flanking regions of nearly half of the genes in maize and many conserved noncoding sequences. Their results also revealed that mCHH islands are enriched for active genes that are located close to terminal inverted repeat (TIR) DNA transposons. These mCHH islands mark a transition for CH and CHG DNA methylation that is associated with transposons. The CHH islands are relatively stable across different tissues, but show some variation among haplotypes, which are often associated with sequence insertions/deletions derived from transposon mobility. These results suggest that mCHH islands specially mark the boundaries between different types of chromatin in the maize genome. The authors further examined mCHH islands in three RdDM mutants 'mop1, mop2 and mop3' and showed that all three mutations greatly reduced mCHH levels. The loss of mCHH islands does not greatly impact gene expression, but instead leads to an additional loss of CG and CHG methylation in some transposons flanking maize genes. These results suggest that RdDM may not be a crucial requirement for the silencing of all transposons. Rather, RdDM activity and mCHH islands may be critical for creating a boundary that prevents the spread of open chromatin from active genes nearby into adjacent transposons. These results shed light on the epigenetically regulated global chromatin in plants. Rachel Wang, 2015

12/2015 Michael Gore
Gerke, JP; Edwards, JW; Guill, KE; Ross-Ibarra, J; McMullen, M. 2015. Genetics. 201:1201-1211
   The genomic impacts of drift and selection for hybrid performance in maize

The work of Gerke et al. (2015) investigated the genomic impact of genetic drift and selection for maize hybrid performance in a reciprocal recurrent selection (RRS) experiment between the Iowa Stiff Stalk Synthetic (BSSS) and the Iowa Corn Borer Synthetic No. 1 (BSCB1) populations. To explore how these two evolutionary forces restructured patterns of genetic variation throughout the breeding history of both populations that were concomitantly selected for combining ability, the progenitor lines and more than 600 individuals across multiple cycles of selection (cycles 0, 4, 8, 12, and 16) were genotyped with a panel of ~40,000 genome-wide SNPs. Through a principal component analysis (PCA) of the SNP marker data set, there was found to be a gradual but continual increase in separation between the BSSS and BSCB1 populations as the experiment progressed along with clear separation of the cycles from one another within each population. This tremendous increase in genetic distance was attributed to the steady loss of genome-wide genetic diversity across cycles of selection within each population. Furthermore, a 10-fold increase in genetic differentiation, as measured by Fst, was found between the founder lines and cycle 16. As supported by computer simulations, most of the reduction in genetic diversity was the result of strong genetic drift imposed by the experimental design, even with selection for the improvement of phenotypes. In addition, the simulations showed that the level of heterozygosity within each population was lower than expected. An identify-by-descent, haplotype-based approach was used to show that the most likely targets of selection were at loci differing between the two populations, which included loci located at the low-recombination, pericentromeric regions of the maize genome. Importantly, such differential patterns of fixation provide better support for the dominance model of heterosis. Michael Gore, 2015

12/2015 Raffaella Battaglia
Bartlett, ME, et al. 2015. Plant Cell. 0:doi: 10.1105/tpc.15.00679
   The maize PI/GLO ortholog zmm16/sterile tassel silky ear1 interacts with the zygomorphy and sex determination pathways in flower development

e functional characterization of the maize class B gene sterile tassel silky ear 1 (sts1) allows the Authors to describe conserved and divergent molecular mechanisms involved in floral organ differentiation and in the establishment of the zygomorphy program in maize flowers. Considering tassel florets, sts1 mutants show the homeotic conversion of the second and third whorls into lemnas/paleae-like structures while in ear florets the Authors describe the homeotic conversion of stamens to carpels. Positional cloning experiments indicate that the sts1 phenotype is due to a mutation in the B class gene Zmmm16, a maize PI/GLO ortholog. As expected, STS1 forms obligate heterodimers with the AP3/DEF orthologs that positively control class B genes expression. As other grass flowers, maize flowers have a single plane of symmetry; while the establishment of the zygomorphy program has been studied in species like A. majus; it is still not clear whether a conserved molecular program occurs in grass flowers. Interestingly, STS1 protein localization experiments, elegantly combined with visualization of auxin dynamics to follow organ initiation, reveal that maize floral phyllotaxis and early B class gene asymmetric expression are directly influenced. Finally, the functional characterization of the B class gene sts1 adds novel data regarding the formation of male and female flowers in maize. In particular, detailed analysis of sts1 expression makes clear that the establishment of floral organ identity controlled by B class genes act upstream of the carpel abortion pathway; in tassel florets, carpel abortion is controlled by the correct organ identity and not position. Raffaella Battaglia, 2015

12/2015 Weibin Song
Sosso, D et al. 2015. Nature Genetics 47:1489-1493
   Seed filling in domesticated maize and rice depends on SWEET-mediated hexose transport

Grain filling is one of the most important traits for crops to translate nutrients into seeds. Investigation on genetics factors controlling the trait will accelerate the genetic improvement in crops. In this study, Sosso and colleagues find a new and effective way to discover the evidence of genomic selection loci related to sugar transport. To identify potential targets of selection among genes that encode sugar transport proteins, they searched large-scale expression data for candidates with high expression level during seed development. Of the 54 genes analyzed, 16 were highly expressed in at least one study. Among the highly expressed genes, ZmSWEET4c was the only locus showing evidence of selection during domestication in a genomic study. As SWEETs function in sugar allocation in plants, ZmSWEET4c was made as a candidate for seed filling. Further genome-wide analysis indicated that ZmSWEET4c has lost more nucleotide diversity during domestication, particularly in the promoter and the first-intron regions. The lower nucleotide diversity in the noncoding region and the higher expression levels between 10 and 17 days after pollination (DAP) support that ZmSWEET4c was domestication related gene. Candidate gene association analysis identified significant associations between SNPs in the promoter region of ZmSWEET4c and ten-kernel and total kernel weight. These SNPs explained >4% of the total phenotypic variation for both traits and as much as 11% of their heritability. Notably, zmsweet4c insertion mutants showed dramatic loss of endosperm but slight effect on embryo development, implying ZmSWEET4c is specific to seed filling. Molecular analyses showed that ZmSWEET4c function in hexose translocation in BETL, a key tissue of endosperm responsible for the nutrients absorption. OsSWEET4, homolog of the ZmSWEET4c, in rice functions as a glucose and fructose transporter and was also a target of selection during rice domestication. These results imply that ZmSWEET4c will help us to generate new high-yield maize and rice varieties. Meanwhile, a new strategy for isolating quantitative trait loci with lower phenotypic variation and heritability was provided for researchers in this field. Weibin Song, 2015

11/2015 Michelle Facette
Christensen, SA et al. 2015. Proc Natl Acad Sci, USA 112:11407-11412
   Maize death acids, 9-lipoxygenase-derived cyclopente(a)nones, display activity as cytotoxic phytoalexins and transcriptional mediators

Christensen et al., isolate a new family of compounds from necrotic developing maize tissue infected with southern leaf blight. They term these new compounds 'death acids' which are specific metabolites called oxylipins that produced by lipoxygenases (LOXes). They identify a suite of death acids produced in necrotic maize tissue, and specifically characterize 10-OPEA and related compounds as locally produced phytoalexins that suppress growth of fungal pathogens and insect feeding. 13-Lipoxygenases produce the known phytohormones 12-OPDA and jasmonic acids; whereas 9-lipoxygenases produce 10-OPEA, which had a previously unknown biological function. They further show that 10-OPEA induces the expression of known defense genes in maize. They demonstrate cytotoxicity of the death acids, and go on to show the mechanism of this cytotoxicity is via cysteine proteases. The elegant and comprehensive chemistry here describe new phytoalexins that mediate local defense responses. Michelle Facette, 2015

11/2015 Weibin Song
Mei, X et al. 2015. Mol Gen Genet 290:1819-1831
   Identification and characterization of paternal-preferentially expressed gene NF-YC8 in maize endosperm

NF-Y is a CCAAT-specific transcription factor that involved in the regulation of a majority of genes. Functional analysis showed that the members in this family regulate the root development, flower development, drought tolerance.The NF-Y transcription factors consist of three different subunits (A, B, and C), and more detailed information about these transcription factors in this family were summarized by Tom Laloum (Tom Laloum et al., 2013). In this study, one of the NA-YC transcription factors, named NF-YC8, was characterized genetically using the endosperm and embryo tissues generated by the reciprocal crosses between the inbred lines B73 and Mo17, Zheng58 and Chang7-2, Huang C and 178 (totally 15 NF-YC genes were identified in the maize genome). Expression analysis showed that NF-YC8 was a differential, gene-specific imprinted gene at 14 DAP and persistently imprinted throughout later endosperm development in the B73/Mo17 genetic background. Bisulfite sequencing for NF-YC8 in maize endosperm indicated that the paternal alleles were higher methylated than maternal alleles in the 5' upstream region, and the coding region was highly methylated in CG context. In addition, the protein sequences of these 15 NF-YC members were highly conserved in maize. This is the first description of maize NF-YC genes and their evolution characterization; also the first experimentally demonstrated the molecular characterization and expression pattern of NF-YC8. These results would provide more information for future investigation in maize kernel development. Weibin Song, 2015

11/2015 Carolyn Rasmussen
Galli, M, et al. 2015. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1516473112
   Auxin signaling modules regulate maize inflorescence architecture

Auxin signaling is require for axillary meristem formation and therefore the development of branches and flowers. The authors demonstrate that two AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) proteins, BARREN INFLORESCENCE 1 and 4 have defects in axillary meristem formation. Normally, AUX/IAAs negatively regulate auxin signaling by sequestering AUXIN RESPONSE FACTOR (ARF) transcription factors. In the presence of auxin, the BIF proteins are degraded to release ARFs that then promote transcription. The semidominant mutants in two AUX/IAA genes, Bif1 and Bif4 have defects in axillary meristem formation. The mutations are in the conserved "degron" domain of the corresponding proteins. Mutant BIF1/BIF4 proteins are not degraded in the presence of auxin and they don't release the ARFs. The authors used an in vitro assay to demonstrate that neither mutant protein was degraded in the presence of auxin. Then, they showed that both BIF1 and BIF4 interact broadly with multiple ARFs, and that some of these ARFs in turn bind to the promoter of the transcription factor BA1. The authors propose that BIF1 and BIF4 negatively regulate the transcription of a basic helix loop helix transcription factor, BARREN STALK1 (BA1) which promotes axillary meristem formation. As auxin levels increase in the inflorescence meristem, BIF1 and BIF4 are degraded and BA1 transcription is promoted by the ARFs to produce the axillary meristem. The authors propose that after the axillary meristem is formed, auxin levels decrease inside the axillary meristem and stabilize BIF1/BIF4 to shut off BA1 transcription, thereby establishing a boundary. Carolyn G. Rasmussen, 2015

11/2015 Chung-Ju Wang
Mao, H et al. 2015. Nature Communications 6: 8326
   A transposable element in a NAC gene is associated with drought tolerance in maize seedlings

Drought is currently one of the main constraints to crop production, which is aggravated by climate warming trends. However, identification of the genetic components underlying drought tolerance has proven to be challenging because of its complexity. In this study, Mao et al. analyzed a natural maize population, consisting of 368 inbred lines, using a genome-wide association study (GWAS) approach. By examining seedling survival rates (SR) after a severe drought treatment in six replicated experiments, phenotypic data was correlated with 560k single nucleotide polymorphisms (SNPs) in the population. The authors identified a SNP within the ZmNAC111 gene (GRMZM2G127379) that is significantly associated with plant drought tolerance (determined by the SR at seedling stage). Sequence analysis of ZmNAC111 in 262 inbred lines further showed that an 82-bp miniature inverted-repeat transposable element (MITE) is present in the ZmNAC111 promoter of drought-sensitive genotypes, such as B73 and Mo17. ZmNAC111 encodes a NAC-type transcription factor whose RNA expression is induced by drought conditions. Its induction is more significant in inbred lines without the MITE insertion (MITE-), suggesting that the MITE insertion may repress ZmNAC111 expression, resulting in higher sensitivity of MITE+ maize varieties to drought stress. Indeed, the authors found that the MITE represses ZmNAC111 expression via RNA-directed DNA methylation and H3K9 dimethylation when heterologously expressed in Arabidopsis. In addition, increasing ZmNAC111 expression in transgenic maize enhances drought tolerance at the seedling stage, improves water-use efficiency and induces upregulation of drought-responsive genes (such as NCED3, AFP3 and DREB1D) under water stress. Finally, a comparison of MITE insertion frequencies among teosinte, tropical/subtropical and temperate inbred lines suggests that the MITE insertion occurred after maize domestication from teosinte and spread in the temperate germplasm. Although it is still not clear that ZmNAC111 and its MITE allele can significantly contribute to enhancing maize yields under drought conditions in the field, this study provides a potential starting point for genetic improvements to drought tolerance in maize. Rachel Wang, 2015

11/2015 Michael Gore
Yang, J, et al. 2015. Plant J. 0:DOI: 10.1111/tpj.13029
   Extreme Phenotype-Genome-Wide Association Study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel

Yang et al. 2015 developed a new efficient method for complex trait dissection via a genome-wide association study (GWAS) built on the principles of bulk segregant analysis (BSA) that exploits the genotyping of phenotypically distinct pools constructed with individuals from a large diversity panel that have extreme phenotypes. This method, eXtreme Phenotype-Genome-wide Association Study (XP-GWAS), depends on the quantification of variant allele frequencies within each of the pools, followed by testing for associations between detected variants and the studied phenotypes. Not only does XP-GWAS harness the historical recombination patterns of large diversity panels to impart high mapping resolution while minimizing the number of individuals that need to be genotyped, but it also potentially enriches for rare variants that underlie extreme phenotypes and maximally exploits the most cutting-edge advances in DNA sequencing and genotyping technologies. The utility of XP-GWAS was empirically tested on the complex trait kernel row number (KRN) using a diversity panel of nearly 7,000 maize accessions from which three pools (low KRN, high KRN, and random KRN) were constructed based on reproducible phenotypic data from the Germplasm Resources Information Network (GRIN) database. The three XP-GWAS pools were genotyped using exome sequencing to estimate allele frequencies, resulting in the detection of nearly one million variants with a minimum read depth cutoff of 50X. In addition, these variants tagged nearly 90% of the high confidence maize filtered genes and were not exclusive to exonic regions of the maize genome. Through the implementation of a GWAS, 145 variants that consolidated into 121 1-kb bins distributed across the 10 chromosomes of maize were found to associate with KRN at a false discovery rate of 5%. Notably, the genomic positions for some of these associated variants significantly co-localized with regions previously detected for KRN by more conventional GWAS. Highlighting the level of resolution that it offers, with XP-GWAS it was possible to separate multiple linked QTL and resolve one of them down to a single candidate gene. The XP-GWAS approach will perhaps have its most impact in the detection of causative genes and favorable alleles in orphan crops and understudied plant species that have limited genomic resources but the availability of germplasm collections that have been phenotypically evaluated. Michael Gore, 2015

10/2015 Carolyn Rasmussen
Baute, J, et al. 2015. Genome Biol. 16:168
   Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population

The authors use a recombinant inbred line (RIL) population originating from a cross between B73 and H99 inbred lines to correlate transcript abundance with leaf traits. RNA-sequencing was performed on the most basal 0.5 cm of the division zone (the base of the leaf where division occurs) from leaf four of 103 different RILs and transcript abundance was compared with measurements of leaf and shoot traits. The traits measured were final leaf size traits (length, area, width and weight), shoot traits (dry and wet weight of the entire above-ground tissue) as well as dynamic growth conditions of the leaf such as leaf elongation rate, leaf elongation duration, the timing of leaf emergence and other events. Intriguingly, a positive correlation between the size of the division zone and final leaf size traits was observed, suggesting that differentially expressed genes within the division zone may be relevant targets for crop improvement. Analysis was focused on the top 1% of correlating or anti-correlating ((anti-)correlating) genes between traits. Of the 1740 genes with expression patterns that (anti-)correlated with at least one trait, ~50% were specific for just one trait. Interestingly, genes with expression levels that (anti-)correlated with final leaf size traits, dynamic leaf traits and shoot weights were then placed into functional categories and compared with Arabidopsis thaliana orthologs and their corresponding mutant phenotypes. Although highly divergent genes (those with more than 1.75% single nucleotide polymorphisms) were eliminated from analysis, it is an important step forward in identifying correlations between gene expression levels and leaf and shoot traits for both known and uncharacterized novel genes. Carolyn Rasmussen, 2015

10/2015 Michael Gore
Bian, Y; Holland, JB. 2015. G3 5:2073-2084
   Ensemble learning of QTL models improves prediction of complex traits

QTL data can be found here.

The genetic dissection of complex traits by QTL linkage analysis in experimental populations offers higher mapping resolution (i.e., smaller marker intervals) when harnessing highly saturated linkage maps. However, increased marker densities may also have negative consequences as multicollinearity among tightly linked genetic markers could confound the detection of QTL and estimation of their effects as well as increase the chance of overfitted QTL models with poor predictive performance. Considering this need, Bian and Holland (2015) developed a new ensemble (machine) learning approach¿¿¿the thinning and aggregating (TAGGING) method¿¿¿where a collection of QTL mapping models are individually trained in parallel on a set of disjoint linkage maps of thinned marker density resulting from a stratified sampling approach, followed by the aggregation of their prediction results with a model averaging procedure. The two authors tested the TAGGING method using cross validation of empirical complex trait data (southern leaf blight, plant height, and days to anthesis) from the maize nested association mapping (NAM) panel in the context of two QTL mapping models: (1) joint-family (JF) linkage analysis for multi-family mapping populations, and (2) single-family (SF) QTL analysis for biparental mapping populations. It was found that among the four tested models, the ensemble joint family linkage (EJF), ensemble single family (ESF), JF, and SF, the EJF models provided the highest prediction ability across all traits, thinning intensities, and QTL selection stringency thresholds. Such a result implies that the TAGGING method assisted the JF analysis to better model the genetic architecture of these three complex traits. In addition, TAGGING of JF and SF models consistently reduced both the variance and bias in prediction for all traits and under all selection thresholds. Interestingly, an ensemble model that united predictions from TAGGING-assisted QTL and infinitesimal (GBLUP) models enhanced prediction abilities, suggesting that the ensembling of both models parlayed complementarities for a truer depiction of the genetic architectures. Taken together, TAGGING has the high potential to provide insights into the genetic architecture of complex traits (QTL position and corresponding effect sizes along with their precision) while improving prediction ability in genetic studies and breeding programs, all of which anchored to highly dense linkage maps. Michael Gore 2015

10/2015 Weibin Song
Grimault, A, et al. 2015. Plant J. 0:doi: 10.1111/tpj.13024
   ZmZHOUPI, an endosperm-specific bHLH transcription factor involved in maize seed development

The embryo and the endosperm could be used as the ideal targets for the study of gene interaction. In this study, the authors identified one bHLH transcription factor named ZmZOU. This gene was the homolog of AtZOU in Arabidopsis. Expressing analysis showed that ZmZOU was the endosperm specific. During maize kernel development, ZmZOU exhibited a high expression level between 9 and 35 days after pollination (DAP) with a peak at 20 DAP. This corresponds to the end of the early development phase (1 to 12DAP) and the entire filling stage (12 to 35 DAP). Within the kernel, ZmZOU expression was limited to the endosperm. Although no precise spatial expression pattern could be established within the endosperm, additional qRT-PCR experiments on the top and bottom and adaxial and abaxial parts of the kernel clearly demonstrated that the expression domain of ZmZOU is much more extensive than that of the ZmEsr2 and ZmLec1 marker genes for the ESR and the embryo, respectively. Transgenic ZmZOU-RNA interference (RNAi) lines were generated with RNAi constructs under the control of the constitutive rice Actin promoter. Phenotyping of the transgenic lines showed that the t ZmZOU knock down did not significantly modify endosperm growth but slightly impeded embryo growth at early stages. The stomatal development in the leaf was affected in the transgenic line of ectopic expression of ZmZOU. Further protein interaction study revealed that the ZmZOU interacts with ZmICE proteins that were also predicted to encode a bHLH transcription factor, which indicated that ZmZOU form a complex with other members of bHLH class during the activation of downstream genes or DNA binding progress. The results here provided us more information about the function of this family member in maize and the functional diversity between different species. The identification and characterization of the regulated genes by ZmZOU will provide us more information about the genetic basements for the interaction between the embryo and endosperm. Weibin Song, 2015

10/2015 Raffaella Battaglia
Lee, DH, et al. 2015. Plant Cell. 0:doi: 10.1105/tpc.15.00434
   The axial element protein DESYNAPTIC2 mediates meiotic double-strand break formation and synaptonemal complex assembly in maize

The Authors studied the functional roles of the maize DESYNAPTIC2 (DSY2) protein during meiosis, the specified cell division to produce haploid cells during sexual reproduction, and revealed the novel insights in homologous chromosome pairing and meiotic synapsis in plants. The original dsy2 mutant was isolated 30 years ago with sterile phenotype. They first identified the gene by map-based cloning using the Sequenom SNP assay in a F2 population that contained segregated dsy2 mutant and phenotypic wild-type plants. To better understand its role, they utilized super-resolution microscope to examine its subcellular localization and showed that DSY2 protein is located on meiotic chromosome axes as a component of the synaptonemal complex, an important protein complex in meiosis. Examination of serial events during meiotic recombination demonstrated that DSY2 is involved in the DNA double strand break formation, the essential step of homologous chromosome pairing. More importantly, studies showed that loss of DSY2 disrupted the synaptonemal complex assembly as the central element fails to load between the chromosome axes in the dsy2 cells. By yeast-two-hybrid and Bimolecular Fluorescence Complementation experiments, the Authors revealed that DSY2 interacts with the central element protein ZYP1, and this finding accounts for the synaptic phenotype observed in the dsy2 mutant. Therefore, DSY2, a chromosome axis protein, not only mediates DNA double strand break formation, but also bridges the chromosome axis and central element during synapsis. This work presented evidence for the first time of the mechanism for the synaptonemal complex assembly at the molecular level. Raffaella Battaglia, 2015

10/2015 Chung-Ju Wang
Suzuki, M; Sato, Y; Wu, S; Kang, B-H; McCarty, DR. 2015. Plant Cell. 0:doi: 10.1105/tpc.15.00290
   Conserved functions of the MATE transporter BIG EMBRYO1 in regulation of lateral organ size and initiation rate

The shoot apical meristem produces lateral organs in a regular spacing and a regular timing, which in turn determines plant architecture. Studies in diverse plant species have suggested that the ER-localized CYP78A is required for regulating lateral organ initiation, presumably via generating a mobile signal that has not yet been identified. In this study, Suzuki et al. identified a MATE transporter, a new class of genes that is involved in in the pathway. Authors first showed the maize bige1 (big embryo1) mutant exhibited accelerated leaf and root initiation as well as enlargement of the embryo scutellum, that are similar to phenotypes observed in cyp78a mutants in diverse plant species. Studies revealed that Bige1 gene encodes a MATE transporter protein, localized to the proximal, trans-Golgi, indicating a possible role in secretion of a signaling molecule. Interestingly, CYP78A/ZmGe1 gene is upregulated in bige1 mutant embryo, suggesting a role for BIGE1 in feedback regulation of a CYP89A pathway. Authors further showed that Arabidopsis bige1a, bige1b single mutant and bige1a bige1b double mutant exhibited increased rosette leaf number, and their phenotype can be complemented by maize Bige1, showing that the BIGE1 transporter has a conserved function in regulation of lateral organ in plants. Although the mobile signals are still unknown, it is plausible that CYP78A and BIGE1 play roles in biosynthesis and movement of small molecules, respectively. Rachel Chung-Ju Wang, 2015

9/2015 Weibin Song
Feng, Y, et al. 2015. Theor Appl Genet. 0:DOI: 10.1007/s00122-015-2589-7
   Multiple loci not only Rf3 involved in the restoration ability of pollen fertility, anther exsertion and pollen shedding to S type cytoplasmic male sterile in maize

Cytoplasmic male sterility (CMS) has been used for hybrid seed production in maize. However, the molecular mechanisms for CMS, specifically for the S type, are not clear enough. Fertility restoration to CMS-S was considered mainly controlled by a single locus named Rf3, which has been mapped to the long arm of chromosome 2 more than 30 years ago, but not cloned yet. In this study, Feng and colleagues focused on the genome wide analysis of the genetic loci associated with the restoration ability to CMS-S. Three fertility related traits (including pollen fertility, anther exsertion and pollen shedding) were used to GWAS study. Firstly, the correlation analysis among the traits showed that Positive, strong correlations were displayed for pollen fertility investigated under the three environments, and correlations of anther exsertion and pollen shedding under different environments were also significant. The three traits were highly correlated with each other. Then, the genome-wide association mapping for the three traits was investigated, which showed that 19, 3 and 8 significant loci for pollen fertility, anther exsertion and pollen shedding were identified, respectively. Individual locus explained up to 28.26 % of phenotypic variation. Of them, only Rf3, the main restorer-fertility gene of CMS-S, was identified for the three traits simultaneously. The results here further verified the complexity of the genetic architecture of fertility restoration to CMS-S, and will accelerate the cloning of the classical restoration gene for CMS-S in maize. Weibin Song, 2015

9/2015 Michelle Facette
Kir, G, et al. 2015. Plant Physiol. 0:DOI: 10.1104/pp.15.00367
   RNAi knockdown of BRI1 in maize (Zea mays) reveals novel functions for brassinosteroid signaling in controlling plant architecture

In this paper, the authors characterize the role of brassinosteroids (BRs) in maize growth by knocking down orthologs of the leucine rich repeat receptor like kinase, BRI1, which has been previously demonstrated in arabidopsis to be the BR receptor. RNAi lines that knock down the maize Bri1 and Bri1-like (BRL) genes plants show defects in growth (such as internode elongation) and BR response, similar to the arabidopsis and rice bri1 mutants. Moreover, kinematic analyses demonstrate that the growth defects are due to both a reduction in cell elongation and cell division. They created a YFP reporter line of the maize ortholog of the BR-responsive transcription factor, BES1. As expected, BES1-YFP was responsive to BR, and interestingly, was enriched in a developing leaves in a band which will eventually determine the auricle and ligule. The RNAi lines also showed a defect in auricle development, resulting in an increase in leaf angle. The RNAi lines shared phenotypes with the maize mutant Rough Sheath-O (Rs-O) and thus determined if BR gene expression was altered in Rs mutants, or vice versa. Expression of marker genes suggested that while there appears to be small changes in BR genes in Rs-O mutants, there was no indication of BR regulating Rs.Together these data work towards a more comprehensive understanding of BR regulation in maize, and how it might contribute to agronomically important traits such as dwarfism and leaf angle. Michelle Facette, 2015

9/2015 Chung-Ju Wang
Svitashev, SK et al. 2015. Plant Physiol 169:931-945
   Targeted mutagenesis, precise gene editing and site-specific gene insertion in maize using Cas9 and guide RNA

Targeted genome editing technologies such as CRISPR/Cas9 utilize engineered nuclease to create targeted DNA double-stand breaks (DSBs), and DSBs can then be repaired by either non-homologous end-joining (NHEJ) or homology-directed repairing (HDR) pathway, depending whether a homologous template is available in the same cell. The NHEJ is prone to imperfect repair, which results in mutations with small deletion or insertions. HDR, on the other hand, can be exploited to achieve precise gene modification by homologous recombination with the desired repair template. The CRISPR/Cas9 system has been shown to function in many plants, including maize. However, these studies reported mutations via NHEJ, rather than precise gene editing. In this paper, Svitashev et al. expressed maize codon-optimized Cas9 endonuclease and single guide RNAs (gRNA) with or without DNA repair template, by biolistic transformation, targeting five different genes in immature maize embryos. Frist of all, by sequencing amplicon at the target sites, the simple Cas9-gRNA experiment without DNA repair template yielded mutation frequencies greater than 1.3 %. It can also simultaneously introduce mutations at multiple loci in a single transformation experiment. They also demonstrated that delivery of gRNA in the form of RNA molecules or DNA vectors into maize cells containing a pre-integrated Cas9 is feasible for the generation of mutations. Then, they tested precise gene editing by co-transforming either single-stranded oligonucleotides or double-stranded DNA vectors as repair templates, and both experiments produced precise single nucleotide change in the ALS2 gene which confers maize plants resistant to chlorsulfuron, an herbicide. Progeny exhibited expected Mendelian segregation of mutations, edits, and targeted gene insertions. This proof-of-principle study nicely demonstrated the utility of Cas9-gRNA technology as a maize genome editing tool. Rachel Chung-Ju Wang, 2015

9/2015 Michael Gore
Technow, F; Messina, C; Totir, LR; Cooper, M. 2015. PLoS One. 10:e0130855
   Integrating Crop Growth Models with Whole Genome Prediction through Approximate Bayesian Computation

When built on accurate whole-genome prediction (WGP) methods, genomic selection (GS) can accelerate the breeding cycle of crops by enhancing genetic gain per unit time. Efforts to improve the accuracies of whole-genome enabled predictions have relied on the development and refinement of linear regression models (e.g., the Bayesian alphabet), maximization of genome-wide marker density, and optimization of training population designs. In contrast to additive effects, the prediction of nonlinear, epistatic effects for complex traits, however, remains a challenge for WGP models. This is especially of concern given that grain yield and other important physiological traits can be the product of both additive and non-additive (multiplicative) effects. Additionally, the ability to predict genotype-by-environment (GxE) interactions for specific environments with WGP models is still in its infancy. To model both non-linear effects and GxE interactions, Technow et al. (2015) incorporated a dynamic crop growth model (CGM), which explicitly incorporates biological and environmental information relating to the physiological mechanisms responsible for crop performance, in WGP of yield as a complex trait in maize. This novel incorporation of a CGM was enabled through the use of an approximate Bayesian computation (ABC) method that replaces a likelihood function with a more tractable simulation step. The performance of the CGM-WGP method for grain yield was superior in terms of prediction accuracy to a standard WGP method without CGM (GBLUP) on a synthetic data set (i.e., simulated genotype and phenotype data for a biparental double-haploid population and observed environmental data across two years) because it better modeled non-additive effects. Notably, the non-additive effects on grain yield were the product of non-linear functional relationships between grain yield and physiological traits. This was especially strong between grain yield and total leaf number, a relationship following an optimum curve. Interestingly, the CGM-WGP method also succeeded at better predicting performance than GBLUP in unobserved environments, as an example, the use of models fitted with 2012 data to predict performance in 2013. Such a result suggested that the CGM-WGP method was more successful at predicting GxE interactions. The findings of this study show that the use of CGM-WGP in the estimation of marker effects across the genome offers higher prediction accuracies than WGP alone, providing a novel method with tremendous potential that can even be further improved with more advanced CGMs and ABC algorithms. The next most important step, however, is to empirically test CGM-WGP in breeding programs of maize and other crops. Michael Gore, 2015

9/2015 Carolyn Rasmussen
Yu, P; Eggert, K; Von Wiren, N; Li, CJ; Hochholdinger, F. 2015. Plant Physiol. 0:DOI: 10.1104/pp.15.00888
   Cell-type specific gene expression analyses by RNA-Seq reveal local high nitrate triggered lateral root initiation in shoot-borne roots of maize by modulating auxin-related cell cycle-regulation

Yu et al demonstrated that locally applied nitrate induced lateral root development by increasing cell division in phloem-pole pericycle cells. Local auxin transport and accumulation of auxin in the stele was observed before lateral root emergence. RNA-sequencing of the stele was used to determine changes in expression patterns between low nitrate and high nitrate conditions. They identified increased expression of positive regulators of the cell cycle (cyclin dependent kinases) and reduced expression of negative regulators of the cell cycle (KRPs) as well as increased expression of several auxin transporters (PIN1a, PIN1c and PIN9) and the ubiquitin dependent protein degradation machinery under high nitrate conditions. Laser capture microdissection was used to show that PIN9 expression increased in endodermis, pericycle and phloem after nitrate treatment while PIN1a expression was increased in the pericycle and the phloem. Their model suggests that high nitrate promotes basipetal auxin transport mediated by PIN1a and PIN1c, while PIN9 transports auxin into pericycle cells. Then auxin directly or indirectly via ubiquitin dependent protein degradation machinery promoted degradation of proteins that block cell cycle progression as well as increased expression of positive regulators of the cell cycle in the stele. This elegant study showed that adult maize roots develop lateral roots in response to nitrate via auxin mediated resumption of cell cycle progression in pericycle cells. Carolyn G. Rasmussen, 2015

8/2015 Carolyn Rasmussen
Nuccio, ML, et al. 2015. Nature Biotechnology. 33:862-869
   Expression of trehalose-6-phosphate phosphatase in maize ears improves yield in well-watered and drought conditions

Several independent multi-year and multi-location field studies were used to demonstrate that maize lines expressing trehalose-6-phosphate phosphatase (TPP) specifically in young ear tissues produced an average of 0.5 metric ton per hectare more than non-transgenic controls under drought conditions. Large increases in yield were observed in well-watered or mild-drought conditions (9%-49%) and severe drought conditions (31%-123%). The increased yield was due to increased sucrose allocation to ear spikelets leading to increased kernel set. TPP converts trehalose-6-phosphate (T6P) to trehalose. T6P, a molecule known to coordinate sucrose levels with plant development via negative regulation of the protein kinase SnRK1, was reduced in plants expressing TPP while sucrose was increased. To reduce pleotropic effects that would be caused by global TPP expression, a rice transcriptional regulator Mads6 promoter was used to express TPP in the following parts of the ear: the node, vasculature and spikelet. Use of another promoter with similar but lower expression in the ear node and vasculature had a detrimental effect on yield. Importantly, rigorous field tests were done over multiple years, locations and germplasm adapted to the field locations to show that OsMads6-TPP1 significantly and consistently increased yield, particularly in drought conditions. Carolyn G. Rasmussen, 2015

Transgenic OsMads6-TPP1, over expressed in ears, results in higher yields, especially under drought conditions.

8/2015 Michelle Facette
Hurni, S, et al. 2015. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1502522112
   The maize disease resistance gene Htn1 against northern corn leaf blight encodes a wall-associated receptor-like kinase

The authors identify the gene Htn1, which confers resistance to the maize pathogen that causes Northern Leaf Blight (NLB). A dominant allele of Htn1 was identified from a Mexican land race of maize, and together with other Htn loci this gene confers resistance to many commercial lines. Map-based cloning of the Htn1 gene identified a region containing two wall-associated kinases (WAKs), and a third, related protein that has the extracellular domain of WAKs but not the intracellular kinase domain. Using the parental mapping lines that contain the resistant Htn1 allele, the authors isolated multiple TILLING mutants in each of the two WAKs, and analyzed these lines for NLB resistance. From this analysis they concluded one of the WAKs (ZmWAK-RLK1) was responsible for NLB resistance. Comparison of the protein sequence in the resistant line to a susceptible line showed that while the intracellular kinase domains are very similar, the extracellular (receptor) domain was diverged. The discovery of a WAK as a resistance protein suggests that it may either act as a receptor that detects fungal- or plant-derived molecules that act as elicitors. Alternatively, since WAKs bind to cell walls, which is a novel property amongst plant receptors, this WAK may directly detect cell wall alterations caused by fungal penetration. Further analysis of this important gene allele will surely forward our understanding of plant-pathogen interactions and the relationship between cell walls and plant defense. Michelle Facette, 2015

8/2015 Michael Gore
Lipka, AE, et al. 2013. G3. 3:1287-1299
   Genome-wide association study and pathway-level analysis of tocochromanol levels in maize grain

Table S7 of the paper lists SNPs associated with 4 tocopherol/tocotrienols grain traits.

Tocochromanols, a group of structurally related compounds that include tocopherols and tocotrienols, are the predominant lipid-soluble antioxidants in maize grain. For each of these two compound classes, there are four species (alpha, beta, delta, and gamma) of compounds distinguished by the degree and position of methyl groups on an aromatic ring. Of these eight compounds, alpha-tocopherol has the greatest vitamin E activity, but tocotrienols appear to have greater antioxidant capacity. Although overt vitamin E deficiency is rare, an estimated more than 90% of Americans have a diet that is insufficient in vitamin E. Notably, suboptimal dietary intake of vitamin E has been linked to increases in risk to cardiovascular disease and some cancers. Maize grain and its derivative oil products primarily consist of the lower vitamin E activity gamma tocopherol, thus genomics-assisted breeding efforts are needed to increase levels of alpha-tocopherol. Through a genome-wide association study and pathway level analysis of a 281-member maize inbred panel scored with more than a half million SNP markers, Lipka et al. 2013 identified key loci controlling levels of tocochromanols in maize grain. Even though the panel did not provide sufficient statistical power at the genome-wide level to detect rare causative alleles from tropical germplasm, a new association between ZmVTE1 (tocopherol cyclase) and tocotrienol composition was detected along with the identification of a ZmVTE4 (gamma-tocopherol methyltransferase) haplotype that had a nearly six-fold difference in alpha-tocopherol levels between least and most favorable haplotype classes. In the pathway-level analysis, ZmHGGT1 (homogentisate geranylgeranyltransferase) and a prephenate dehydratase parolog (one of four in the maize genome) were found to modestly regulate tocotrienol levels. The allelic variation at these four loci have the potential to be harnessed in maize biofortification breeding programs for optimizing the profile of vitamin E and antioxidant levels in grain. Michael Gore, 2015

8/2015 Chung-Ju Wang
Wang, H; Studer, AJ; Zhao, Q; Meeley, RB; Doebley, JF. 2015. Genetics. 200:965-974
   Evidence that the origin of naked kernels during maize domestication was caused by a single amino acid substitution in tga1

Maize is remarkably dissimilar to its wild ancestor teosinte, which makes it an extremely interesting model for the study of domestication. A single gene, teosinte glume architecture1 (tga1), encoding a SBP-box transcriptional regulator, has been identified as the gene conferring encased teosinte kernels into naked maize kernels. In this study, Wang et al showed that a single fixed nucleotide difference between maize and teosinte in the tga1 coding sequence, leading to an amino acid substitution (Lys in teosinte to Asn in maize at the sixth amino acid position), is the causal variant that underlies the origin of the naked maize grains. The protoplast transient assays with effector and reporter constructs showed that Lys-Asn substitution makes the maize-TGA1 a strong transcriptional suppressor. Although maize -TGA1 and teosinte-TGA1 show no difference on binding site specificity for the GTAC motif, maize-TGA1 was found to form more stable dimers than teosinte-TGA1. Authors also explained their previous observation that higher TGA1 protein abundance detected in teosinte is likely due to a tightly linked paralog of tga1, called not1, whose protein product can be also recognized by the anti-TGA1 antibody. Together with the fact that the not1 null allele has no phenotype, these results support the model that the single amino acid substitution in TGA1 controls this kernel trait between maize and teosinte. Authors also described the pleiotropic effects of RNAi lines for tga1, indicating that tga1 may play a broad role in development. Interestingly, tga1-RNAi maize plants display some characteristics of the tga1-teosinte glume phenotype, suggesting that Lys-Asn from teosinte to maize is a gain-of-function mutation. This paper showed a nice example how a simple amino acid change can alter protein function and thereby drive morphological evolution. Rachel Wang, 2015

8/2015 Raffaella Battaglia
Shi, JR et al. 2015. Plant Physiol pp.doi: 10.1104/pp.15.00780
   Over-expression of ARGOS genes modifies plant sensitivity to ethylene, leading to improved drought tolerance in both Arabidopsis and maize

The Authors investigate the functional role of the maize and Arabidopsis ARGOS genes. As a first approach they over-express the Zm-ARGOS1 gene in Arabidopsis obtaining transgenic plants with a phenotype similar to the ethylene insensitive mutants ethylene response 1 (etr1-1) and ethylene-insensitive 2 (ein2-1). To better understand whether the Zm-ARGOS1 gene might be involved in the ethylene pathway, the Authors analyze the phenotype of 35S:Zm-ARGOS1 seedlings germinated in presence of ethylene or its precursor 1-aminocyclopropane-1-carboxylic acid (ACC). Interestingly, the 35S:Zm-ARGOS1 plants are insensitive to exogenous ethylene. The ethylene insensitiveness is further confirmed with different approaches and also testing the Zm-ARGOS8, At-ARGOS-LIKE2 (At-ARL2) and At-ARL3 genes. Next, Shi and colleagues aim to understand whether the Zm-ARGOS1 gene acts in the ethylene pathway. They therefore introduce the 35S:Zm-ARGOS1 construct into the ctr1-1 mutant background where the ethylene signal is suppressed. The results that they obtain indicate that the signaling pathway downstream of CTR1 functions properly even in the presence of over-expressed Zm-ARGOS1. In wild-type plants, the activity of the ethylene receptor in modified by the interaction of the REVERSION-TO-ETHYLENE-SENSITIVITY1 (RTE1) and ETR1 factors. The observation that the ethylene insensitive phenotype decreases when the Zm-ARGOS1 gene is over expressed in the etr1-7 rte1-2 double mutant background makes the Authors suggest that Zm-ARGOS1 may act between the ethylene receptor and CTR1, affecting ethylene perception or the early stages of ethylene signal transduction. Arabidopsis plants over expressing the Zm-ARGOs genes show increased drought tolerance and, interestingly, the over expression of the Zm-ARGOS8 gene in maize leads to increased grain yield under field conditions. Raffaella Battaglia 2015

8/2015 Weibin Song
Grimault, A et al. 2015. Plant Sci 236:116-125
   Role of B3 domain transcription factors of the AFL family in maize kernel filling

The trait of kernel filling is important for yield, and many QTLs have been identified using different linkage population. But no QTLs controlling the kernel filling were cloned so far. In this paper, Grimault et al. characterized the functional roles of the AFL gene family members (belonging to B3 domain transcription factor) during the kernel filling stage. Among the five ZmAFL genes identified in the maize genome, ZmAFL4, like LEC2, has preferential gene activity in pollen and seed, although its seed gene activity is restricted to the endosperm during reserve accumulation. Knock down of ZmAFL4 gene activity perturbs carbon metabolism and reduces starch content in the developing endosperm at 20 DAP. ZmAFL4 and ZmAFL3/ZmVp1 trans-activate a maize oleosin promoter in a heterologous moss system. These results suggest that the functions of some members of this family could be conserved between dicot and monocot species, and provided us many new candidates for further research the complex trait: kernel filling. Weibin Song, 2015

7/2015 Michael Gore
Chandler, KL, et al. 2013. Crop Sci. 53:189-213
   Genetic Analysis of Visually Scored Orange Kernel Color in Maize

Maize is an important staple crop in many of the countries where vitamin A deficiency is present and has considerable genetic variation for carotenoid grain levels. However, the varieties of maize grain typically used for human consumption do not provide adequate daily levels of provitamin A carotenoids. White grain maize has minimal levels of carotenoids and it is highly preferred over yellow maize for human consumption in East and southern Africa. Yellow grain maize has appreciable levels of carotenoids, but is viewed as inferior in these countries due in part to its negative association with imported relief food, animal feed, and unfavorable taste and texture. However, recent studies are showing that there does not appear to be strong aversion to orange maize that has higher levels of provitamin A carotenoids. Chandler et al. (2013) showed that orange kernel color has a heritable basis, and a significant proportion of the phenotypic variation in this color trait appears to be regulated by QTL proximal to carotenoid biosynthesis and degradation genes. Results from this study provide evidence that orange kernel color should respond favorably to visual selection for increasing total carotenoids and can be further enhanced by marker-assisted selection of carotenoid synthesis and degradation genes directly influencing composition to increase provitamin A levels in maize grain. Michael Allen Gore, 2015

7/2015 Michelle Facette
Redkar, A et al. 2015. Plant Cell 27:1332-1351
   A Secreted Effector Protein of Ustilago maydis Guides Maize Leaf Cells to Form Tumors

Ustilago maydis is a biotrophic fungus that infects many different maize tissues. Like all pathogens, U. maydis secretes effector molecules that help promote the infection and colonization process. In turn, these effectors are sometimes recognized by the plant, and promote defense responses. This paper characterizes the U. maydis secreted effector protein See1, and it's interactions in maize. The authors determine the See1 effector is required for induction of leaf tumors in maize; but not tassel or ear tumors. Transcriptomic analyses and analysis of DNA synthesis in infected tissues indicate a role for See1 in promoting DNA replication in infected tissues. A yeast 2-hybrid screen revealed that See1 interacts with the maize ortholog of SGT1, a regulator of cell cycle progression previously shown to be involved in defense responses in plants. The authors confirm this interaction using immunoprecipitation and BiFC, and show that See1 and SGT1 localize to the cytoplasm and nucleus in plant cells. They further show that See1 interferes with the phosphorylation of SGT1 in planta, thus suggesting a molecular mechanism for infection. Specifically, they suggest that the suppression of SGT1 phosphorylation by See1 results in suppression of defense responses and/or promotion of the cell cycle. Michelle Facette, 2015

Other maize Genes possibly involved in the interaction reported in this paper are: maize MAPK kinase 2, NP_001104843.1; maize putative MAPK family protein, AFW85791.1; maize putative MAPK MPK6, ACG37232.1; maize ABA stimulation MAPK, NP_001152745.1; maize unknown kinase, ACF85409.1. maize MAPK kinase 2, NP_001104843.1; BLASTs to GRMZM2G020216 (98% ident). Second hit GRMZM2G002100 (92% ident.) maize putative MAPK family protein, AFW85791.1; BLASTs to GRMZM2G020216 (100% ident). Second hit GRMZM2G002100 (94% ident.) maize putative MAPK MPK6, ACG37232.1; BLASTs to GRMZM2G020216 (99% ident). Second hit GRMZM2G002100 (93% ident.) maize ABA stimulation MAPK, NP_001152745.1; BLASTs to GRMZM2G002100 (98% ident). Second hit GRMZM2G020216 (93% ident.) maize unknown kinase, ACF85409.1. BLASTs to GRMZM2G002100 (100% ident). Second hit GRMZM2G020216 (94% ident.)

7/2015 Weibin Song
La Rocca, N, et al. 2015. J Exp Bot. 0:doi:10.1093/jxb/erv278
   The maize fused leaves1 (fdl1) gene controls organ separation in the embryo and seedling shoot and promotes coleoptile opening

Seedling architecture is more related to the embryo development, and some genetic mutation during the embryogenesis will affect the seedling architecture, as cr4 and dek1 mutant affected both the seedling leaf and kernel in maize. In this study, Nicoletta and colleagues have cloned and characterized the mutant fdl1-1 that was isolated by an Enhancer/Suppressor mutator (En/Spm) element insertion located in the third exon of the gene, identifies a novel gene encoding ZmMYB94, a transcription factor of the R2R3-MYB subfamily. This gene has been cloned through co-segregation analysis, and verified by the RNAi method. Further analysis showed that Fdl1 is involved in the regulation of cuticle deposition in young seedlings as well as in the establishment of a regular pattern of epicuticular wax deposition on the epidermis of young leaves. loss of Fdl1 action also correlates with developmental defects, such as delayed germination and seedling growth, abnormal coleoptile opening and so on. qPCR indicated that high expression was observed in the embryo, in the seedling coleoptile and in the first two leaves, whereas RNA level, as well as phenotypic defects, decreases at the third leaf stage. Interestingly several of the Arabidopsis MYB genes most closely related to ZmMYB94 are also involved in the activation of cuticular wax biosynthesis, suggesting deep conservation of regulatory processes related to cuticular wax deposition between monocots and dicots. Since several MYB genes in maize are involved in the control of the phenylpropanoid metabolic pathway, Fdl1 has provided a new role of ZmMYB family members during the maize embryo development for us. Weibin Song, 2015

7/2015 Chung-Ju Wang
Mascheretti, I et al. 2015. Plant Physiol 168:1351-1363
   Florigen-encoding genes of day-neutral and photoperiod-sensitive maize are regulated by different chromatin modifications at the floral transition

It has been known that floral regulatory pathway, including autonomous, and photoperiod controls the expression of florigen genes, and in turn promotes the transition from vegetative to reproductive development via long-distance trafficking from leaf to the shoot apical meristem. Maize is considered to be either a day-neutral plant (such as the temperate maize line B73) or a short-day plant (such as tropical maize lines). Teosinte, the maize progenitor found in tropical environments, is also sensitive to day lengths and its transition from vegetative to reproductive development can be induced by short-day treatment. In maize, the ZCN8 gene was shown to have florigenic activity. The indeterminate1 (id1) gene, encoding a zinc finger protein, is known to promote the ZCN8 expression in mature leaf of B73. However, ZCN8 gene is unlikely a direct target of ID1, because they are expressed during different stages of leaf development. On the other hand, in tropical maize, the short-day photoperiod is able to induce ZCN8 gene expression. These different floral induction controls in maize provide a unique opportunity to study mechanisms regulating ZCN gene expression between the autonomous and photoperiod pathways. In this study, the expression and associated-epigenetic markers of two maize florigen genes (ZCN7 and ZCN8) were studied in B73 (normal flowering), the id1 mutant (unable to flower), and tropical teosinte under floral-inductive and non-inductive photoperiods. Mascheretti et al revealed that histone H3 acetylation in ZCN7/ZCN8 chromatin are associated with competence to flower in response to id1 gene activity in temperate B73. However, in teosinte, different histone markers (H3K4me2, and H3K4me3) are associated with floral-inductive teosinte samples. Finally, authors proposed a model that in temperate maize, id1 is expressed in developing leaves to establish a transcriptionally competent chromatin state that later allows expression of ZCN7/ZCN8 in mature leaf. In tropical maize, floral induction is dependent on short-day photoperiods and the circadian clock to activate florigen expression via epigenetic control on different histone modifications. Chung-Ju Rachel Wang, 2015

7/2015 Raffaella Battaglia
Nelissen, H et al. 2015. Plant Cell pp.doi: 10.1105/tpc.15.00269
   Dynamic Changes in ANGUSTIFOLIA3 Complex Composition Reveal a Growth Regulatory Mechanism in the Maize Leaf

The Authors study the changes in composition of the AN3-associated SWI/SNF complex in diving and expanding cellular domains of the maize leaf. The Tandem Affinity Purification (TAP) approach is used to purify the proteins associated to the ANGUSTIFOLIA3 (AN3/GIF1) factor in different areas of the growing maize leaf; the purified proteins are then analyzed on a mass spectrometer. Interestingly, the Authors identify a core complex that is highly conserved between eukaryotes; this complex is then recruited to the target DNA by growth process-specific GROWTH REGULATING FACTORS (GRFs). While the GRF1 factor is highly represented as associated AN3 protein in dividing tissues, the GRF4 and GRF10 factors are more abundant in expanding tissues. The model proposed by the Authors show that, in the maize leaf, the balance between different GRFs associated to the AN3/GIF1 factor determines the transition between diving and expanding tissues. Together with elucidating the molecular processes occurring in the growing maize leaf, the paper from Nelissen et al. puts the basis to improve the study of protein complexes with a dynamic perspective. Raffaella Battagila, 2015

7/2015 Carolyn Rasmussen
Zhan, A et al. 2015. Plant Physiol pp.DOI:10.1104/pp.15.00187
   Reduced lateral root branching density improves drought tolerance in maize

The authors compared maize recombinant inbred lines (RILs) that had many short lateral roots to those RILs that had few but long lateral roots under water stress conditions. RILs with few but long lateral roots had a greater ability than RILs with many short lateral roots to acquire water under water stress conditions. The ability to acquire water provided the plants with few long lateral roots with better drought tolerance, which was assessed by comparing leaf relative water content, yield, carbon dioxide exchange, and root respiration under well watered and water stress conditions. They also measured the isotopic ratios of water to see where in the soil the plant's water was acquired. The few but long lateral roots were able to gather water from deeper within the soil, which allowed increased plant growth and yield. Importantly, the authors used three distinct environments to perform water stress experiments: a greenhouse mesocosm, and two spatially separated fields. The results showed the same trends in all three environments suggesting that few and long lateral roots may provide better water acquisition across different soil types and other environmental factors. In almost every case the phenotype of the roots were consistent across different environmental conditions indicating genetic control of this phenotype. Together, these data suggest that the few but long lateral root phenotype may be helpful for improving drought tolerance in maize. Carolyn Rasmussen, 2015

6/2015 Carolyn Rasmussen
Li, F et al. 2015. Plant Cell 27:1389-1408
   Autophagic recycling plays a central role in maize nitrogen remobilization

Autophagy serves to recycle components of the cytoplasm including organelles by targeting them to the vacuole for degradation thereby freeing nitrogen for other uses. This paper demonstrates the important role of autophagy for nitrogen remobilization during seed production. RNA-sequencing demonstrated that autophagy genes are ubiquitously expressed but upregulated in mature maize leaves and roots and endosperm suggesting that proteins are being recycled upon senescence. Coexpression analysis suggested that certain autophagy pathway isoforms may work together in specific tissue types. Annotation of the authophagy pathway revealed several single copy genes including autophagy-related 12 (atg12) and 2 Uniform-Mu insertions provided mutants in atg12. ATG12 is a ubiquitin fold protein that acts together with ATG5 and ATG 16 to ligate ATG8 to the lipid phophatidylethanolamine which aids in trafficking autophagosomes to the vacuole. atg12 mutants show reduced ATG8 lipidation and fail to accumulate YFP-ATG8 in autophagic bodies even under nitrogen or fixed-carbon limitation. Plants lacking ATG12 have reduced seed yield in nitrogen sufficient conditions and premature leaf senescence, and more severe phenotypes during nitrogen limitation. The reduction in seed yield is due to defects in nitrogen remobilization efficiency to the seeds in atg12 mutants demonstrated by nitrogen partitioning assays. Together, these results demonstrate the important role of autophagy in nitrogen remobilization during development and seed production. Carolyn G. Rasmussen, 2015

6/2015 Raffaella Battaglia
Li, C et al. 2015. Plant Cell 27:532-545
   Genome-Wide Characterization of cis-Acting DNA Targets Reveals the Transcriptional Regulatory Framework of Opaque2 in Maize

opaque2 (o2) mutant maize kernels have been described few decades ago due to their higher lysine content compared to wild-type kernels. The phenotype is due to a mutation in a bZIP transcription factor; a modified version of the o2 mutation later led to the development of Quality protein maize (QPM) with important repercussion for the production of high-yield and high-protein maize. In this paper, Chaobin and collaborators combine genome-wide approaches as RNA-seq and ChiP-seq to i) compare the transcriptome of o2 maize endosperm with wild-type endosperm and ii) identify direct target genes of the O2 protein. O2 appears to be a key factor in plant metabolism controlling the transcription of different zeine genes, genes involved in endosperm carbon portioning, stress resistance genes and transcription factors. Interestingly, lncRNAs are indirectly activated by O2. Furthermore, novel O2 binding sites are identified by the authors. Raffaella Battaglia, 2015

6/2015 Michael Gore
Lu, F, et al. 2015. Nature. 6:6914
   High-resolution genetic mapping of maize pan-genome sequence anchors

Data can be downloaded here: here.

Genotyping by sequencing (GBS), a current standard genotyping platform for maize, is a reduced-representation approach, sequencing at high density the subset of low-copy genomic regions tagged by cut sites of a selected restriction enzyme (Elshire et al. 2011). With the plummeting of DNA sequencing costs, ultra-high density genotyping has now become a reality and can even enable assembly of pan-genomes. However, extensive structural variation is present in maize, including transposable and other repetitive elements, copy number variation (CNV), presence/absence variation (PAV), inversion, and translocation. These variable expansions, contractions, and rearrangements complicate alignment of diverse whole-genome sequences into an assembled maize pan-genome, which is useful for understanding and leveraging extant variation. The study of Lu et al. (2015) marks a hinge point in maize genomics through its use of high-quality, mapped GBS sequence tags to anchor the assembly of a maize pan-genome. This study used GBS to sequence more than 14,000 maize inbred lines, resulting in 1.3 trillion bp of sequence at an average depth of 0.3 reads per site per sample. By implementing the GBS bioinformatics pipeline, ~26 million GBS tags were identified, and from these tags nearly 700,000 SNPs were identified and scored across all the lines. Then, two genetic mapping approaches (GWAS and joint-linkage mapping) were used to test for association between individual SNP genotypes and the PAV pattern of each GBS tag. In sum, ~22 million sequence tags were initially mapped to the genomic position of the SNP with which each tag showed strongest association, but ~35% were mapped to the incorrect chromosome.

As a result, machine learning (ML) models trained on uniquely aligned B73 tags (UABTs) mapped by JL, GWAS, or both were developed to predict map accuracy and identify accurately mapped tags for the selection of high-quality sequence anchors for the maize pan-genome. The application of three M5Rules ML models selected 4.4 million GBS tags with mapping accuracies lending themselves well to serving as unique sequence anchors. Illustrating the challenge of short-read sequence alignment in a complex genome such as that of maize, MiSeq paired end sequencing of 95 diverse inbreds was used to assess the accuracy of alignments for the 4.4 million tags, and estimated a 20% error rate in alignment for 150 to 300 bp reads. Notably, 26% of the selected tags were classified as PAVs, suggesting that B73 contains only ~74% of the low-copy sequence of maize. Additionally, 89% of the 1.1 million PAV tags absent from the B73 reference genome were found to be present in the genome assembly of the deeply sequenced maize inbred line, CML247. In general, PAVs were more frequently found in pericentromeric regions and showed a positive correlation with repeat density. SNPs associated with PAVs were found in additional GWAS of over 2,000 diverse inbreds to be enriched for significant associations in four agronomic traits. This finding supports a hypothesis that has driven efforts to assemble a pan-genome, that structural variation is also functional, and further suggests the high gains to be made from these efforts. Michael Allen Gore, 2015

This paper reports the deep SEQUENCING and assembly of the maize inbred CML247.

6/2015 Chung-Ju Wang
Yu, CP, et al. 2015. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1500605112
   Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors

The gene regulatory network that controls maize leaf development is still not well understood. This knowledge may be useful for developing C3 crops to perform C4 photosynthesis for enhanced yields in a long run. In this study, Yu et al studied 22 transcriptomes of developing maize leave from dry seeds to 192 hours post imbibition. Through coexpression and differential gene expression analysis, authors identified functional transitions with molecular signatures during leaf development. Interestingly, authors analyzed expressions of transcription factors (TFs) among 22 samples, and highlighted the key TF families involved in developmental and physiological processes. More significantly, authors used maize genomic sequences and transcriptomic data or used the known TFs and its transcription factor binding sites (TFBS) in rice and Arabidopsis to predict maize TF-TFBS pairs during leaf development. In total, about 1300 novel TFBSs and 253 new TF-TFBS pairs were identified in maize. This dataset will serve as the foundation for a systems biology approach to the understanding of regulatory network involved in maize leaf development. Rachel Wang, 2015

Chun-Ping and colleagues use an extensive data set to finely describe the transcriptional changes that occur during leaf development in maize. The authors analyze 22 transcriptomes with a time span from hour 0 (dry seeds, T000) to 192 h post imbibition (T192). The possibility of having this large dataset allows to precisely identify genes that are coregulated and involved in the same biological processes. 30 co-expressed modules are divide into three stages and different criteria are used to define Differentially Expressed Genes (DEGs). Focusing on Transcription Factors (TFs), the authors describe not only the expression dynamic of single TF but they also consider TF gene families in their whole. This approach takes into consideration the functional redundancy that can be shared between members of the same TF gene family and identify TF gene families predominantly expressed at specific developmental stages. An interesting result described in the paper is the prediction of Transcription Factor Binding Sites (TFBSs) and their cognate TF. The large number of transcriptomes that are analyzed in the paper and the establishment of stringent selection criteria are used to infer sets of strongly coexpressed genes and to predict TFBSs. Combining different methods, Chun-Ping and collaborators identify 253 new TF-TFBS pairs in maize. Altogether, the results described contribute to better understand the regulatory circuit that occurs during maize leaf development. Raffaella Battaglia, 2015

6/2015 Weibin Song
Xing, A, et al. 2015. J Exp Bot. 0:doi: 10.1093/jxb/erv182
   A rare SNP mutation in Brachytic2 moderately reduces plant height and increases yield potential in maize

The plant height is known as an important trait during maize breeding progress, many QTLs and several mutants corresponding to the plant height have been reported. But few QTL has been cloned and functional studied. In the present study, Xing et al. reported the fine mapping and cloning of the major plant height QTL, qph1, using a RIL population and the near-isogenic lines. The qph1 was narrowed down to a 1.6 kb interval on maize chromosome 1. In that interval, a mutant site was fund in the coding sequence of the Brachytic2 gene that has been characterized for ten more years. The naturally occurring rare SNP in qph1 resulted in an amino acid substitution and was validated as the causative mutation. Association analysis among 527 inbred lines using the SNP showed that the mutant site produced a rare allele. QPH1 protein is located in the plasma membrane and polar auxin transport is impaired in the short near-isogenic line RIL88 (qph1). Allelism testing showed that the SNP variant in qph1 reduces longitudinal cell number and decreases plant height by 20% in RIL88 (qph1) compared to RIL88 (QPH1), and is milder than known br2 mutant alleles. The effect of qph1 on plant height is significant and has no or a slight influence on yield in four F2 backgrounds and in six pairs of single-cross hybrids. Moreover, qph1 could reduce plant height when heterozygous, allowing it to be easily employed in maize breeding. Overall, the new allele with less-severe effect on the plant height has great potential in maize genetic improvement. Weibin Song, 2015

5/2015 Weibin Song
Li, P et al. 2015. J Exp Bot 0:doi: 10.1093/jxb/erv127
   A genetic relationship between nitrogen use efficiency and seedling root traits in maize as revealed by QTL analysis

Root system architecture (RSA) is characterized by their roles in anchorage and absorption of nutrients and water, and ability to respond dynamically to the soil environment. Many studies have demonstrated the ability of maize to alter growth patterns in order to explore for and utilize nutrient such as nitrogen. But the genetic relationship between RSA and nitrogen use efficiency (NUE) traits remains largely unkown. In this study, the authors investigated the genetic basis of RSA and NUE traits in maize using a recombination inbred line population that was derived from two lines contrasted for both RSA and nitrogen use efficiency traits. The authors performed the QTL identification at the conditions of high-nitrogen and low-nitrogen, and totally 10 NUE- and 9 RSA-related traits were evaluated in four field environments and three hydroponic experiments, respectively. Based on the phenotypic analysis, the nitrogen uptake efficiency (NupE) had significant phenotypic correlations with RSA, especially for the traits of seminal roots and crown roots, the main components of the mature root structure. Further QTL analysis indicated that 331 quantitative trait loci (QTLs) were detected. Among these QTLs, five important QTLs clusters at the chromosomal regions bin1.04, 2.04, 3.04, 3.05/3.06, and 6.07/6.08 were found in which QTLs for both traits had favourable effects from alleles coming from the large-rooted and high-NupE parent. Some of the QTL with positive effect will increase the grain yield using the advanced backcross-derived lines. Generally, understanding the genetic basement will contribute the genetic improvement of the root structure and the nitrogen utilization. The larger effect QTL that identified in the present study could be used as candidates for further cloning the RSA and NUE related genes. Weibin Song, 2015

5/2015 Michael Gore
Chung-Ju Wang
Rodgers-Melnick, E et al. 2015. Proc Natl Acad Sci, USA 112:3823-3828
   Recombination in diverse maize is stable, predictable, and associated with genetic load

Within the context of crop improvement, recombination is the evolutionary engine of plant breeding populations, providing new allelic combinations on which artificial selection can act for fixation in or purging from the population. The efficiency of selection is especially increased when recombination breaks up associations between favorable and deleterious variants. With this in mind, Rogers-Melnick et al. (2015) explored the highly variable landscape of recombination in the US and Chinese (CN) maize nested association mapping (NAM) populations, with each NAM population consisting of multiple biparental families connected through a common female parent (B73 for US, Huangzaosi for CN). Through analysis of genotyping-by-sequencing (GBS) data, 136,000 cross-over events were identified at high resolution and their frequencies found to be highly predictable between populations and across families. Notably, cross-over rate was found to be negatively associated with CpG methylation, and repeat content, resulting in suppression of cross-over events in pericentromeric regions and enrichment in subtelomeric regions. In some families, recombination was found to be suppressed over non-pericentromeric regions spanning one or more megabases; this pattern was tentatively attributed to inversions through examination of maize/sorghum synteny. Through a Bayesian modeling approach, recombination hotspots (i.e., intervals of crossover enrichment) were identified, ranging in size from 1 to 30 kb that were highly conserved between both NAM populations. Relative to control regions, these hotspots showed distinct patterns of higher prevalence of hypomethylation as well as higher mean GC content and GC-biased gene conversion. Genomic evolutionary rate profiling (GERP), which infers the history of purifying selection acting on a nucleotide site from a multi-species comparison, revealed that hotspots had a lower genetic load (fewer deleterious alleles) than the genome-wide average. The present constraints of recombination severely limit the purging of deleterious alleles, which perhaps can only be efficiently conducted through breeding with technologies that can increase the global recombination rate (i.e., QTL or transgenes for increased recombination rate) and edit the genome for both nucleotide and methylation patterns. Michael Gore, 2015

Maize is notable for its genetic diversity within the species as the average genetic distance between two inbred lines exceeds that between human and chimpanzees. These allelic variations provide a large number of allelic combinations for breeding. On the other hand, shuffling linkage groups to purge deleterious alleles or to combine all the preferable genes requires meiotic recombination. It has been known that recombination can vary over 1000-fold across the maize genome. In this study, Rodgers-Melnick et al analyzed markers by genotyping-by-sequencing (GBS) within US and Chinese maize nested association mapping (NAM) populations to map a total of 136,000 recombination breakpoints- where crossovers occurred. They found that the pattern of crossovers is highly predictable, for example, CpG methylation has a strong negative relationship with the crossover density. By comprising crossover sites among lines, recombination hotspots were identified and found to be historically stable across two diverse sets of maize germplasm. They also found that the regions of the maize genome with the lowest recombination rates accumulate the largest number of deleterious alleles. This finding suggested that these portions of the maize genome may harbor undesirable genes that will be difficult to be removed by conventional breeding techniques. Rachael Chung-Ju Wang, 2015

5/2015 Raffaella Battaglia
Yu, CP, et al. 2015. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1500605112
   Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors

The gene regulatory network that controls maize leaf development is still not well understood. This knowledge may be useful for developing C3 crops to perform C4 photosynthesis for enhanced yields in a long run. In this study, Yu et al studied 22 transcriptomes of developing maize leave from dry seeds to 192 hours post imbibition. Through coexpression and differential gene expression analysis, authors identified functional transitions with molecular signatures during leaf development. Interestingly, authors analyzed expressions of transcription factors (TFs) among 22 samples, and highlighted the key TF families involved in developmental and physiological processes. More significantly, authors used maize genomic sequences and transcriptomic data or used the known TFs and its transcription factor binding sites (TFBS) in rice and Arabidopsis to predict maize TF-TFBS pairs during leaf development. In total, about 1300 novel TFBSs and 253 new TF-TFBS pairs were identified in maize. This dataset will serve as the foundation for a systems biology approach to the understanding of regulatory network involved in maize leaf development. Rachel Wang, 2015

Chun-Ping and colleagues use an extensive data set to finely describe the transcriptional changes that occur during leaf development in maize. The authors analyze 22 transcriptomes with a time span from hour 0 (dry seeds, T000) to 192 h post imbibition (T192). The possibility of having this large dataset allows to precisely identify genes that are coregulated and involved in the same biological processes. 30 co-expressed modules are divide into three stages and different criteria are used to define Differentially Expressed Genes (DEGs). Focusing on Transcription Factors (TFs), the authors describe not only the expression dynamic of single TF but they also consider TF gene families in their whole. This approach takes into consideration the functional redundancy that can be shared between members of the same TF gene family and identify TF gene families predominantly expressed at specific developmental stages. An interesting result described in the paper is the prediction of Transcription Factor Binding Sites (TFBSs) and their cognate TF. The large number of transcriptomes that are analyzed in the paper and the establishment of stringent selection criteria are used to infer sets of strongly coexpressed genes and to predict TFBSs. Combining different methods, Chun-Ping and collaborators identify 253 new TF-TFBS pairs in maize. Altogether, the results described contribute to better understand the regulatory circuit that occurs during maize leaf development. Raffaella Battaglia, 2015

5/2015 Carolyn Rasmussen
Chettoor, AM; Evans, MMS. 2015. Frontiers Plant Sci. 0:doi: 10.3389/fpls.2015.00187
   Correlation between a loss of auxin signaling and a loss of proliferation in maize antipodal cells

Within the female gametophyte (embryo sac), the antipodal cells are likely to produce and distribute auxin in the ovule. The embryo sac contains several different cells including the egg cell, synergids, central cell and the antipodal cells. The authors mined data from RNA sequencing of embryo sac enriched samples and compared them to ovule samples in which the embryo sac was removed. The embryo sac enriched samples have higher mRNA expression levels of multiple components of the auxin biosynthesis, transport and signaling pathways compared to the surrounding ovule. The phylogenetic tree of several families was displayed with over represented mRNAs highlighted, a useful way to visualize the relationship between gene relationship and expression patterns. In an interesting comparison, the Auxin Response Family (ARF) gene family was displayed with both ARF family members targeted by artificial microRNAs that caused embryo sac development defects in Arabidopsis thaliana, with those overrepresented in the embryo sac in maize. One class of ARFs, Class II, was most overrepresented in maize embryo sacs, but was not targeted by the artificial microRNAs in A. thaliana, making correlations between expression and previous functional analysis difficult. To determine which cells within the embryo sac were responding to auxin, PIN1a-YFP, an auxin efflux transporter and pDR5-RFP, an auxin responsive promoter fused to RFP, were used to determine which cells contributed to the increased mRNA expression of auxin in the embryo sac. Although the PIN1a-YFP patterns were variable, they were concentrated with the antipodal cells as was the pDR5-RFP signal. Finally, in a dominant mutant that alters both embryo sac development and abaxial leaf polarity called Laxmidrib1-O (Lxm1), PIN1a-YFP and pDR5-RFP expression was reduced in the antipodal cells as was the number of antipodal cells. Intriguingly, the expression of pDR5-RFP was also lower in the nucellus, part of the ovule, in Lxm1 suggesting that the source of auxin for the nucellus may come from the antipodal cells. This is an important paper because little is known about the function of antipodal cells and their persistence during development within the grasses. The authors propose that auxin may be playing a role in antipodal cell proliferation and potentially that antipodal cells may promote proper seed development. Carolyn Rasmussen, 2015

4/2015 Carolyn Rasmussen
Zoschke, R; Barkan, A. 2015. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1424655112
   Genome-wide analysis of thylakoid-bound ribosomes in maize reveals principles of cotranslational targeting to the thylakoid membrane

In this study, the authors use a large-scale "ribosome profiling" approach to clarify how plastid encoded proteins are targeted to the thylakoid membrane. Plastid encoded proteins are targeted to the thylakoid membrane via two distinct processes that depend strongly on the structure of the protein. When the transmembrane domain is located within 80 amino acids of the end of the protein, the protein is posttranslationally targeted to the thylakoid membrane. In contrast, if the transmembrane domain or signal sequence is further than 80 amino acids from the stop codon, it is targeted to the membrane as it is being translated (cotranslationally targeted). The method used to deduce this rule for thylakoid membrane targeting is called ribosome profiling. Maize leaf mRNAs are separated into soluble and membrane fractions, then treated with ribonucleases. If the mRNA is inside the ribosome, it is protected from degradation by ribonucleases. The small, protected fragments of the mRNA are called the ribosome footprint, and they were hybridized to a tiling microarray to determine their sequence and location. If ribosome footprints were partitioned into the membrane fraction, the newly formed peptide was inserted into the membrane as it was translated. Two exceptional cases were identified. The first exceptional case is the only protein that contains a chloroplast signal peptide, PetA. In this case, the signal peptide, not the transmembrane domain, is determinant for co-translational membrane targeting. The other case is the only plastid-encoded protein that localizes to the inner envelope membrane, CemA. Although the mechanism is unknown, the transmembrane domains of this protein do not target the mRNA to the thylakoid membrane, suggesting that the lysine rich CemA specific sequence prevents thylakoid membrane insertion. After global analysis, the rules for plastid encoded protein targeting to the thylakoid membrane were identified and it is likely that these rules can be extended to bacterial proteins. Carolyn G. Rasmussen, 2015

4/2015 Chung-Ju Wang
Zhai, J et al. 2015. Proc Natl Acad Sci, USA 112:3146-3151
   Spatiotemporally dynamic, cell-type-dependent premeiotic and meiotic phasiRNAs in maize anthers

In this study, Zhai et al. found that two distinct classes of phased small-interfering RNAs (phasiRNAs) are transcribed during maize anther development. By small RNA profiling of 10 stages of maize anthers, authors identified that 21-nt phasiRNAs from 463 loci appear abruptly after germinal and somatic cell specification, whereas 24-nt phasiRNAs from 176 loci accumulate during meiosis. Interestingly, in situ hybridization and sequencing of RNA from several anther developmental mutants demonstrated that 21-nt phasiRNAs biogenesis triggered by miR2118 requires a functional epidermis, and 21-nt siRNAs then likely move to all the cell layers of anthers. In contrast, miR2775 triggers the biogenesis of 24-nt phasiRNAs, and 24-nt siRNA all accumulate preferentially in tapetum and meiocytes. This finding revealed an interesting spatial-temporal control of two classes of phased siRNAs. Their particular abundance in reproductive organs resembles the piRNA in mammals. piRNAs are a conserved class of small RNAs that are found during male reproductive stages in animals. It had been notable that piRNAs are absent in plants, yet this finding suggests a putative convergent evolution to produce small RNAs in reproductive organs. Rachel Chung-Ju Wang, 2015

4/2015 Michael Gore
Wallace, JG, et al. 2014. PLoS Genetics. 10:e1004845
   Association mapping across numerous traits reveals patterns of functional variation in maize

One of the more difficult challenges facing biology in the 21st century is pinpointing the causative variants responsible for natural phenotypic variation in organisms. The tremendous genetic and phenotypic diversity of maize complemented by its extensive genetic and genomic toolbox make it a powerful model system for the genetic dissection of complex trait variation. In this light, Wallace et al. (2014) conducted a genome-wide association study (GWAS) in the U.S. maize nested association mapping (NAM) panel for 41 different phenotypes that covered a range of genetic complexity. Through forward-regression GWAS with the high-resolution HapMap v. 1 and 2 data set [28.9 million single-nucleotide polymorphisms (SNPs) and nearly 800,000 copy-number variants (CNVs)], remarkably only 4,484 SNPs and 318 CNVs were found to be significantly associated with at least one of the traits tested. The strongest class enrichment was for genic SNPs and CNVs, especially synonymous SNPs and large CNVs. However, almost 70% of the ~4800 variants resided outside of annotated genes (gene-proximal, within 5kb of a gene; or intergenic, more than 5 kb away from a gene) in the likely vicinity of promoters and regulatory elements. This study also found that minor allele frequency and standardized effect size generally had an inverse relationship that was consistent across variant classes. That is, rarer, larger-effect variants from the intergenic class tended to explain a smaller amount of unique variance in each trait than did more common, smaller-effect variants from the genic and gene-proximal classes. Genes related to regulatory activity and those that had a paralog were found to be enriched for GWAS associations, whereas genes with low expression values and involvement in core metabolic functions showed slight depletion even though 14 metabolite traits were included in the analysis. While it remains a major challenge to identify the causative variants controlling a phenotype, the results of this study suggest that expanding the variant search space to include the still-inadequately annotated non-genic regions of the complex maize genome is needed. Michael Gore, 2015

4/2015 Weibin Song
Yi, G; Neelakandan, AK; Gontarek, BC; Vollbrecht, E; Becraft, P. 2015. Plant Physiol. 167:443-456
   The naked endosperm genes encode duplicate ID domain transcription factors required for maize endosperm cell patterning and differentiation

In this study, the authors showed us the cloning and functional analysis of the two unlinked genes encoded by the INDETERMINATE domain transcription facor, and the two genes are homologous genes distributed on chromosome 2 and 10, respectively. Knocking down or knocking out either gene will show naked endosperm (nkd) phenotype. Phenotypic analysis revealed that the aleurone cell differentiation was disrupted in the nkd mutant, and also resulted in reduced filling in the mutant seed. Positional cloning method was used to isolate the two genes, and additional alleles were found to confirm that the candidates were corresponded to nkd1 and nkd2. Expressing patterns of the two genes showed that the NKD transcripts accumulated higher around 11 to 16 day after pollination. Subcelular localization showed that the fused protein of NKD-GFP was found in the nuclei of the onion. Finally, the data presented by Yi and colleagues provided us new insight into understanding the aleurone cell differentiation in maize. Weibin Song, 2015

4/2015 Raffaella Battaglia
Zhan, J, et al. 2015. Plant Cell. 0:513-531
   RNA Sequencing of Laser-Capture Microdissected Compartments of the Maize Kernel Identifies Regulatory Modules Associated with Endosperm Cell Differentiation

In this paper the Authors describe the molecular networks that control cell differentiation in specific filial and maternal compartments of the maize kernel. The expression profile of cells dissected from Aleurone (AL), Basal Endosperm Transfer Layer (BETL), Embryo-Surrounding Region (ESR), Conducting Zone (CZ), Central Starchy Endosperm (CSE), Embryo, Nucellus, Placento-Chalazal region, pericarp and vascular region of the pedicel at 8 Days After Pollination (DAP) allowed to identify compartments-specific genes. These results are the starting point to define modules of co-expressed genes and gene regulatory networks (GRNs) that regulate kernel differentiation both temporally and spatially. The statistical analysis of RNA-seq data indicate that at least 18 coexpression modules (M1- M18) can be described in the developing kernel at 8 DAP. Focusing the attention on endosperm, the Authors identify cis-regulatory elements enriched in the promoter region of genes belonging to each coexpressed module. Interestingly, within a BETL coexpressed module, a large subset of genes are direct target of the Myb-Related Protein-1 (MRP-1) factor. As a whole, the data presented by Zhan and colleagues represent a clear dissection of the network occurring in a model system, as the developing maize endosperm, which also represents an important resource for food, feed and raw material. Raffaella Battaglia, 2015

3/2015 Carolyn Rasmussen
Facette, MR et al. 2015. Nature Plants 0:Article number: 14024
   The SCAR/WAVE complex polarizes PAN receptors and promotes division asymmetry in maize

This paper identified the dependence of the leucine-rich repeat receptor-like kinases PANGLOSS1 (PAN1) and PAN2 on one of the regulators of branched actin nucleation called the SCAR/WAVE regulatory complex (WRC) in an asymmetric division leading to the formation of the stomata in maize. The stomatal complex is formed through the development of a guard cell bordered on two sides by two small triangle shaped subsidiary cells. The subsidiary cells are formed by an asymmetric division of the subsidiary mother cell (SMC), which is preceded by actin accumulation and nuclear movement toward the guard mother cell (GMC). In maize, it was previously shown that one member of the WRC, called BRICK1 because its pavement cells lacked crenulations and resembled bricks, also had an role in SMC divisions. Other mutants (brk2 and brk3) with similar defects in both pavement cell crenulation and subsidiary cell division were previously characterized, but their genetic identity was previously unknown. This paper identified maize BRK3 as a component of the WRC, and further identified a complex containing all five components of the WRC by co-immunoprecipitation followed by mass spectrometry. Next, the genetic relationship between the WRC and PAN1 and PAN2 was analyzed When mutants in the WRC, brk1 and brk3, are combined with pan1 or pan2 mutants, they have a synergistic effect on subsidiary cell development (up to ~90% abnormal) suggesting non-overlapping or convergent roles in subsidiary cell development. Using the developmental gradient of the maize leaf, a clear relationship between the GMC length and the developmental stages of the SMC, and localization of fluorescently tagged proteins in mutants, the authors identified epistasis relationships between the WRC, PAN1, PAN2, the monomeric small GTPase RHO GTPASE OF PLANTS (ROPs), as well as actin patch formation and nuclear polarization. After formation of the guard mother cell, BRK1 (which is a proxy for the entire WRC) localizes first to the SMC and indirectly recruits PAN1 and PAN2 to the SMC; PAN1 and PAN2 failed to localize to the SMC in either brk1 or brk3 mutants. This result is significant because it suggests branched actin networks polarize PAN2 and PAN1. Then, as previously described, PAN1 directly recruits ROP2 to the SMC and activates it leading finally to actin patch and nuclear polarization. Based on these observations the authors suggest a model where the SCAR complex first is responsible for polarizing PAN receptors, and then later PAN receptors activate SCAR to stimulate actin patch formation. Carolyn Rasmussen, 2015.

3/2015 Raffaella Battaglia
Yang, F, et al. 2015. Plant Cell. 0:doi: 10.1105/tpc.114.130393
   A maize glutaredoxin gene, abphyl2, regulates shoot meristem size and phyllotaxy

The Authors describe a yet unknown mechanism controlling meristem size and phyllotaxy in maize. The identification of the new dominant maize mutant Aberrant phyllotaxy2 (Abph2) allowed Yang and colleagues to demonstrate that a GLUTAREDOXIN (GRX) gene plays a role in the regulation of SAM size and phyllotaxy. In the Abph2 genetic background, an active copy of the MALE STERILE CONVERTED ANTHER1 (MSCA1) gene appeared to be transposed in the Abph2 locus and misexpressed during embryo development. As a result, mutant plants showed an enlarged meristem and a decussated phyllotaxy. MSCA1 encodes a GLUTAREDOXIN protein, a redox regulator, proposed to post transcriptionally regulate transcription factors. Using genetic approaches and molecular analysis, the Authors indicate the FASCIATED EAR4 (FEA4) factor as a candidate target controlled by MSCA1. The MSCA1 gene has been already described as a regulator of anther development in maize, the fact that a GRX protein is involved in SAM size determination and phyllotaxy was presumably masked by functional redundancy with two close homologs identified on the maize genome. It is now challenging to understand how hormones and redox signals crosstalk to determine SAM size and phyllotaxy. Raffaella Battaglia, 2015

3/2015 Michael Gore
Technow, F, et al. 2014. Genetics. 197:1343-1355
   Genome properties and prospects of genomic prediction of hybrid performance in a breeding program of maize

Commercial hybrid maize breeding has been traditionally reliant on per se and testcross performance results to select superior inbred line parents, suspending the evaluation of experimental hybrids for ultimately the final stage of the breeding cycle. Genomic prediction of hybrid performance when combined with contemporary advances in double haploid, genotyping, and phenotyping technologies finally offers the potential to identify superior single-cross hybrids at the early stages of the breeding pipeline. As perhaps a glimpse into the not-so-distant future of breeding maize hybrids, Technow et al. (2014) analyzed genotypic and phenotypic data collected from 1,254 single-cross maize hybrids built on Dent x Flint heterotic patterns that had been in part evaluated over 14 years and 20 locations in Southern Germany. Statistical examination of the genome-wide SNP marker data revealed a high concordance in linkage phases but major differences in allele frequencies between the Flint and Dent heterotic groups at pericentromeric regions of maize chromosomes. It is at these recombinationally suppressed pericentromeric regions where the Hill-Robertson effect is likely to be strongest. Such findings support differential fixation of alleles due to pseudo-overdominance - repulsion phase linkage between QTL alleles - at pericentromeric regions as a major contributor to the genetic basis of heterosis. Genomic prediction of grain yield and moisture with two different statistical models was highest for untested hybrids when both parents were parents of other hybrids in the training set, and in contrast, lowest when neither parent contributed to training set hybrids. How best to optimize the size and composition of the training set, particularly in relation to population and family structures, is still an ongoing research question. As these findings illustrate, identifying the best hybrid - a pursuit initiated more than 100 years ago by G. H. Shull - now has a better chance of becoming an early-stage venture. Michael Gore, 2015

3/2015 Weibin Song
Zuo, W et al. 2015. Nature Genetics 47:151-157
   A maize wall-associated kinase confers quantitative resistance to head smut

Head smut is a systemic fungal disease caused by S. reilianum that occurs in most maize-growing areas and causes tremendous loss of yield. In this study, Zuo et al isolated a major QTL, qHSR1, corresponding to the resistance to maize head smut using a classical strategy of map-based cloning. Sequencing and transgenic complementation demonstrated that the resistance gene encoding a receptor-like kinase in maize named ZmWAK (wall-associated kinase) . The functions of WAK and WAK-like proteins have been investigated deeply in other plants such as Arabidopsis, and these genes mainly involved in plant development, signaling perception and transduction and including plant defense. ZmWAK was highly expressed in the mesocotyl of seedlings where it arrested biotrophic growth of the endophytic S. reilianum. Domestication analysis of ZmWAK, including the spread in maize germplasm has been also performed. Taken together, these results provide us both a model for resistance QTL cloning and a new strategy to control head smut for maize breeders. Weibin Song, 2015

3/2015 Chung-Ju Wang
Pautler, M, et al. 2015. Plant Cell. 0:doi 10.1105/tpc.114.132506
   FASCIATED EAR4 encodes a bZIP transcription factor that regulates shoot meristem size in maize

The stem cells in shoot apical meristem (SAM) are capable of generating founder cells for organ initiation and self-renewing to maintain its own cell numbers. The balance between self-renewal of central stem cells and organ initiation from peripheral cells is controlled by dynamic, complex signaling networks, for example the well-characterized CLV-WUS negative feedback pathway. In this study published by Pautler et al, a fasciated ear mutant, fea4 was isolated. Unlike most of previously identified fasciated ear genes, such as fea2, td1 and ct2, which are directly involved in the CLV pathway, FEA4 acts in parallel to the CLV pathway. FEA4 encodes a bZIP transcription factor, as a negative regulator of meristem size. Its RNA is present in the peripheral zone of the SAM, and in the vasculature of young leaves it is excluded from the stem cell niche. Both double mutant analysis and transcriptome profiling suggested that FEA4 is not directly involved in the CLV pathway. Finally, ChIP-seq and RNA-seq experiments revealed that FEA4 may regulate gene expression that are involved in auxin response pathway and other homeobox transcription factors to accelerate differentiation in the peripheral zone. Rachel Wang, 2015.

2/2015 Raffaella Battaglia
Li, XJ, et al. 2014. Plant J. 79:797-809
   Small kernel1 encodes a pentatricopeptide repeat protein required for mitochondrial nad7 transcript editing and seed development in maize and rice

In this study, the Li et colleagues describe the role of C to U editing in mitochondria transcripts. The characterization of the maize small kernel 1 (smk1) mutant allows the Authors to correlate mitochondrial complex I assembly, seed development and nad7-836 transcript editing. Smk1 is a nuclear gene encoding a mitochondrion-targeted PPR-E subclass protein that is required to specifically edit the mitochondrial nad7-836 transcript and to create a leucine codon at position 279; a loss of editing in mutant plants leaves a proline codon. This gene is ubiquitously expressed, nevertheless mutations in Smk1 mainly affect kernel formation; embryo and endosperm development is delayed with approximately 90% of the mutant kernels being completely lethal. Analysis of the mitochondrial protein complexes and morphological studies reveal that the loss of nad7-836 editing in the smk1 mutant disrupts complex-I assembly thus leading to abnormal mitochondrial biogenesis. Interestingly, specific protein domains within the PPR-E subclass proteins are highly conserved across species. Focusing on the orthologous rice Os_Smk1 gene, the Authors highlight the functional conservation between the maize and rice Smk1 genes showing that demonstrate that the nad7-836 editing function is critical to embryo and endosperm development in both species. Raffaela Battaglia, 2015

2/2015 Michael Gore
Rincent, R et al. 2012. Genetics 192:715-728
   Maximizing the Reliability of Genomic Selection by Optimizing the Calibration Set of Reference Individuals: Comparison of Methods in Two Diverse Groups of Maize Inbreds (Zea mays L.)

Genomic selection is a breeding approach that has shown promise in plants to accelerate the breeding cycle by enhancing genetic gain per unit of time through the early selection of nonphenotyped individuals (selection candidates or validation set) that show favorable genomic signatures for targeted traits. Essentially, a set of molecular markers is used to predict breeding values for individuals based only on their marker genotypes. The prediction of breeding values is founded on a statistical model that has been calibrated (or trained) on the phenotypes and genotypes of reference individuals (reference population or calibration set). Importantly, the size and composition of the calibration set are some of the critical parameters that directly impact the reliability of predictions (the correlation between predicted and true breeding values). In that light, Rincent et al. (2014) tested several methods to maximize the reliability of genomic predictions through optimally selecting individuals to comprise the calibration set based on marker data alone. These methods were tested on two independent maize diversity panels (one Dent and one Flint) that had been genotyped with a 50k SNP array and phenotyped for three traits (male flowering time, plant biomass, and dry matter content) with differing levels of heritability. Specifically, the performance of two metrics used to select calibration sets for optimized genomic prediction reliability were compared. The generalized coefficient of determination (CD) accounts both for error variances of the marker-based predictions (PEV) and for the potential reduction in genetic variance due to relatedness (i.e., prevents the selection of very closely related individuals). An optimized selection algorithm based on the CD mean was found to impart higher reliabilities for the three traits in both panels across a number of calibration set sizes compared to use of the PEV mean alone, which does not penalize for high relatedness. These results suggest that the CD mean algorithm can be used to efficiently optimize the composition of calibration sets, allowing for an increase in genomic prediction reliability with a concomitant decrease in the number of reference individuals needed to be phenotyped. Michael Gore, 2015

2/2015 Carolyn Rasmussen
Johnston, R, et al. 2014. Plant Cell. 0:doi: 10.1105/tpc.114.132688
   Transcriptomic analyses indicate that maize ligule development recapitulates gene expression patterns that occur during lateral organ initiation

A global analysis of the transcripts was performed to identify genes that are specifically enriched or underrepresented found in the developing ligule. Laser-microdissection, in which a specific set of cells is removed, was used to isolate cells from developing ligule and surrounding blade and sheath and followed by RNA-sequencing. As a control, equivalent tissue was also dissected from a mutant that does not form a ligule, liguleless1 (lg1). A set of 34 genes with higher transcript levels in the developing ligule also had reduced transcript abundance in the lg1 mutant suggesting that these transcripts are specific for the ligule. Intriguingly, many of the genes that had high transcript levels in the developing ligule were transcription factors that have been previously identified in lateral organ patterning or leaf initiation such as narrow sheath 1 and several Class III Homoedomain leucine zipper (HD-ZIPIII) genes. Boundary specification genes such as the maize homologs of CUP-SHAPED COTEYLEDON2 and BLADE-ON-PETIOLE1/2 had enriched transcript levels in developing ligules. When in situ hybridization was used to confirm the expression patterns, these transcripts and others were observed not only in developing ligules, but also at lateral organ boundaries. Partners of KNOX homeobox transcription factors, BEL transcription factors 12 and 14, are also expressed in the developing ligule. A model is proposed where auxin from the developing blade restricts homeobox transcription factors to the developing ligule and sheath to specify the blade-sheath boundary. Carolyn Rasmussen, 2015

2/2015 Chung-Ju Wang
Chuck, GS; Brown, PJ; Meeley, RB; Hake, S. 2014. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1407401112
   Maize SBP-box transcription factors unbranched2 and unbranched3 affect yield traits by regulating the rate of lateral primordia initiation

The number of lateral primordia made by the male and female inflorescences of maize is a major determinant of yield, since it dictates tassel branch number (TBM) and ear row number (ERN). In this study, Chuck et al identified SBP-box transcription factors, unbranched2 (ub2) and unbranched3 (ub3) that share similarity with tasselsheath4 (tsh4), a gene responsible for repression of leaf primordia in maize inflorescences. Double mutants of ub2 and ub3 display a decrease in TBM and an increase in ERN. SEM on tassels further showed that many extra tows of spikelet pair meristems are initiated with extra leaves at the base of the tassel. Taken together, these results suggest that ub2 and ub3 function together to limit the rate of lateral primordia initiation in the wild-type. Immunolocalization of UB2 and UB3 proteins found accumulation throughout the meristem but absence from the central domain of the meristem where cells regenerate. Interestingly, the ub3 locus is tightly linked to QTL for ERN and TBM in both the nested association mapping (NAM) and intermated B73 by Mo17 (IBM) populations of maize recombinant inbreds, suggesting this gene may be agronomically important. Rachel Wang, 2015.

1/2015 Carolyn Rasmussen
Thompson, BE et al. 2014. Plant Cell 26:4702-4717
   The dicer-like1 homolog fuzzy tassel is required for the regulation of meristem determinacy in the inflorescence and vegetative growth in maize

In this study, fuzzy tassel was identified as a partial loss of function dicer-like1 mutant in maize. The dcl1-fzt mutant was caused by a S-to-N substitution in the RNAse IIIa domain. Not surprisingly, dcl-1 loss-of-function alleles are embryo lethal, whereas those with non-silent amino acid substitutions in the helicase domain were morphologically normal. Pleotropic phenotypes of dcl1-fzt mutants include disordered inflorescence architecture, sex determination defects, short stature and narrow leaves. The mutant phenotypes appear to be caused by reduction in microRNA (miRNA) levels, which is caused by failure to appropriately process many but not all miRNA precursors. An elegant aspect of this study is the analysis of phenotypes based on the relative reduction in levels of miRNAs known to alter developmental programs. Strong defects in meristem determinacy were correlated with significant reductions (>25-fold) in the levels of miR172e/ts4. miR172e has already been implicated in regulating meristem determinacy through analysis of the tasselsheath4 mutant. Another intriguing result was that, dependent on inbred background, the phase change (whereby juvenile leaves transition into adult leaves) was either delayed or faster in the dcl1-fzt mutant compared to wild-type siblings. This is discussed in the context of relative levels of the opposing activities of two miRNAs miR156 and miR172 on phase changes. Carolyn Rasmussen, 2015.

1/2015 Chung-Ju Wang
Gent, JI, et al. 2014. Plant Cell. 0:doi: 10.1105/tpc.114.130427
   Accessible DNA and relative depletion of H3K9me2 at maize loci undergoing RNA-directed DNA methylation

The maize genome is notable for its numerous transposons and repeat sequences, and those regions are often tightly packed and stained densely under microscopes, named as heterochromatin. Heterochromatin formation is implicated in gene silencing with presence of specific chromatin modifications, such as histone H3K9me2 or H3K27me2. Studies in yeast have shown that RNA-directed DNA methylation (RdDM) pathway is involved in heterochromatin formation; however, multiple studies in plant genomes suggested that RdDM is not a uniform feature of heterochromatin. The relationship between RdDM and heterochromatin in plants is unclear. In this study, Gent et al compared several heterochromatic features, including H3K9me2 and H3K27me2, chromatin accessibility, DNA methylation and small RNAs in maize wild type as well as two mutants affecting DNA methylation, one functions independently of RdDM and the other is a key component of RdDM. Their results revealed that the majority of the genome exists in a heterochromatic state defined by inaccessible chromatin that is marked by H3K9me2 and H3K27me2 but lacks RdDM. The minority of the genome marked by RdDM appeared more similar to euchromatin than to heterochromatin. This data indicated that heterochromatin differs fundamentally from RdDM-targeted chromatin. Authors further proposed that small interfering RNAs perform a specialized role in repressing transposons in accessible chromatin environments and that the bulk of heterochromatin is incompatible with small RNA production. Rachel Wang 2015.

1/2015 Michael Gore
Owens, BF, et al. 2014. Genetics. 198:1699-1716
   A foundation for provitamin a biofortification of maize: Genome-wide association and genomic prediction models of carotenoid levels

A genome-wide association study and pathway-level analysis were carried out for 24 individual and derived carotenoid traits, permitting the detection of four major-effect loci including novel associations for zep1 (zeaxanthin epoxidase) and lut1 (a cytochrome P450 required for carotenoid epsilon-ring hydroxylation) in maize. These combined approaches ascribed maize paralogs to various enzymatic steps in the carotenoid and isoprenoid biosynthesis pathways that were previously only characterized by model species. In addition, it was demonstrated that markers in the vicinity of such a priori candidate genes underlying quantitative trait loci (QTL) yielded similar prediction accuracies for carotenoid grain traits as compared to a genome-wide set of markers. Such results suggest that a small number of genes responsible for carotenoid biosynthesis and retention can be effectively employed in marker-assisted selection. Michael Allen Gore, 2015

12/2014 Madelaine Bartlett
Haag, JR et al. 2014. Cell Reports 9:378-390
   Functional diversification of maize RNA polymerase IV and V subtypes via alternative catalytic subunits

Eukaryotes have three essential DNA-dependent RNA polymerases: Pol I, II, and III. Plants are distinct from other eukaryotes in possessing two additional polymerases, Pol IV and V, that synthesize RNAs involved in silencing transposons, repetitive elements, and some genes. In addition, Pol IV, and possibly Pol V, has been implicated in the epigenetic phenomenon of paramutation. Maize has a number of homologs for all of the Pol IV and Pol V components known from Arabidopsis thaliana, but the exact composition of the full twelve-subunit complexes has remained unclear. This paper describes significant advances in characterizing both Pol IV and Pol V of maize in detail. Eleven of the twelve subunits were recovered for each polymerase, and, unexpectedly, the two protein complexes are differentiated only by the identity of the largest subunits. This is not the case in A. thaliana, where there is a discriminatory Pol V-specific 5th subunit. A second interesting result is that maize has multiple subtypes of both Pol IV and Pol V that appear to be functionally distinct. This paper raises interesting questions about the historical origins of Pol IV and V, and the results hint at a surprising evolutionary fluidity in the composition of two important protein complexes. Madelaine Bartlett, 2014.

12/2014 Andrea Gallavotti
Lewis, MW et al. 2014. Development 141:4590-4597
   Gene regulatory interactions at lateral organ boundaries in maize

The angle at which leaves are borne is an important architectural feature in plants. Modern maize varieties have been selected for upright leaves in order to increase plant density in the field. The regulation of leaf angle is determined at the junction of the sheath and the blade, whereby auricles and ligules regulate leaf angle and protect the stem, respectively. In maize, both the liguleless1 and 2 (lg1 and 2) genes are well known to regulate ligule formation and leaf angle. In this study, Lewis et al. isolated the gene that causes a previously described dominant mutant, Wavy auricle in blade1 (Wab1-R), affected in ligule, auricle and blade formation. To clone the causative gene they combined a traditional map-based cloning approach with an EMS screen for intragenic suppressors. After narrowing the map position to only two transcription factors, the lack of obvious mutations or rearrangements in the region led them to devise a genetic strategy to identify knock-outs in the dominant Wab1-R allele. The isolation of a single revertant with a point mutation in the DNA binding domain of a TCP transcriptional regulator, proved that wab1 encodes the TCP gene. This gene had been independently isolated in a previous forward genetic screen for inflorescence architecture mutants (Bai et al. 2012, PNAS 109:12225-12230). By careful genetic and molecular analysis using both dominant and revertant loss-of-function mutations, Lewis et al. determined that the normal function of wab1 is to regulate the expression of lg1 in the adaxial region at the base of the tassel branches, and that in the dominant mutant this module is activated by the overexpression of wab1 in leaves (of unknown cause). The developmental defects observed in Wab1-R are reminiscent of defects in maintaining boundaries in developing organs, such as those established between the shoot apical meristem and lateral organs (e.g. inflorescence meristem and tassel branches). Given the similar molecular and developmental program observed in the ligular region and at the junction of tassel branches, the authors propose that the ligule functions as a boundary domain in developing leaves. Andrea Gallavotti 2014

12/2014 Candice Hirsch
Stelpflug, SC et al. 2014. Genetics. 198:209-218
   Consistent and heritable alterations of DNA methylation are induced by tissue culture in maize

Extensive phenotypic variation exists in maize and more variation is constantly being generated. One such way is through tissue cultured induced somaclonal variation. It has been well characterized in a number of plant species, including maize, that somaclonal variation exists, and that it generally results in the occurrence of unexpected phenotypes in progeny resulting from tissue culture. Understanding tissue culture induced variation is important as basic research through molecular plant breeding research can utilize tissue culture. In this study, the effect the tissue culture process has on genome-wide DNA methylation patterns of regenerated plants was investigated by generating profiles of DNA methylation in multiple regenerated plants from an inbred line. It was found that numerous regions exhibited altered DNA methylation levels, and that many of the hypomethylation events occurred at the same genomic sites across independent regenerants and cell lines. Additionally, the DNA methylation changes were in many cases heritable after self-pollination. These regions showing differential methylation may respond to more general stresses beyond that experienced during tissue culture as the regions overlapped with previously observed differentially methylated regions. This study provides important insights into not only tissue culture induced variation, but more generally, stress included variation. Candice Hirsch, 2014.

11/2014 Andrea Gallavotti
Dooner, HK; He, L. 2014. Proc Natl Acad Sci, USA. 0:doi:10.1073/pnas.1415482111
   Polarized gene conversion at the bz locus of maize

Most of recombination events in maize are intragenic and can occur with or without crossovers. Gene conversion is the non-reciprocal transfer of information from one chromatid to another, and historically in maize it has been studied by identifying the flanking marker arrangement (usually visual markers) of intragenic recombination events. Gene conversion was shown to be the prevalent mode of recombination between dimorphic heterozygotes, that is alleles that are essentially identical but for one site. In previous studies with the bronze locus (bz) no preference in polarity of conversion, that is the tendency of markers located near one end of the gene to convert more frequently than those located at the opposite end, was observed. This contrasted with findings in fungi where conversion polarity was reported in several cases. Conversion gradients along genes are generally considered to reflect a preferential initiation site for recombination. In this study, Dooner and He used EMS and transposon excision mutagenesis to create a series of new bz alleles in the same genetic background located throughout the length of the gene to determine if preferential conversion at the proximal or distal side was indeed observed. These new alleles were tested in large diallelic crosses to test all possible heteroallelic combinations. In this way they produced several thousand intragenic recombination events of which the majority could be accounted for by gene conversion. The analysis of these events revealed a general trend in conversion with a U-shape, suggesting that conversion initiates preferentially at either the 5' or 3' end of the bz gene but rarely extends to the entire length of the gene. Overall this study suggests that recombination initiation sites within genes are polarized in maize. Andrea Gallavotti, 2014.

11/2014 Candice Hirsch
Hirsch, CN, et al. 2014. Genetics. 198:409-421
   Insights into the effects of long-term artificial selection on seed size in maize

Corn and other cereal crops are a staple food source worldwide. Seed size is an important grain yield component trait that is important in crop domestication as well as in yield improvement. Understanding the molecular mechanisms underlying cereal grain yield is important in providing a stable food source worldwide. Long-term selection experiments hold a wealth of information regarding the genetic architecture of a trait. In this study, pooled whole genome resequencing of the Krug Yellow Dent base population and populations selected for 30 cycles for small and large seed size was used to identify signatures of selection in this long-term selection experiment. In total, 94 signatures of selection were identified. Additionally a large number of copy number variation regions were identified between the extreme populations. In addition to providing insights into the genetic architecture of seed size, this study also supports a general role for non-coding sequences and copy number variation in contributing to response to phenotypic selection. Candice Hirsch, 2014.

11/2014 Madelaine Bartlett
Estep, M, et al. 2014. Proc Natl Acad Sci, USA. 111:15149-54
   Allopolyploidy, diversification, and the Miocene grassland expansion

The grass tribe Andropogoneae includes not only maize, but also a number of plants of key economic importance, including sugarcane, Miscanthus, and Sorghum. This investigation into the phylogeny of the tribe has revealed an extraordinarily high level of allopolyploidy. Allopolyploids arise through genome doubling after a hybridization event between two distinct species. The investigators use gene trees todetect allopolyploids, and find evidence for allopolyploidy in at least 32% of the species sampled. It has been a matter of some debate as to whether polyploidy is a driver of diversification in plants. The position of allopolyploidy events across the dated tree generated in this study allowed the researchers involved to test the diversification hypothesis in the Andropogoneae. What they found was that although allopolyploidy does appear to be a frequent mode of speciation, the vast majority of allopolyploidy events did not result in increased diversification rates. This paper represents an interesting step forward in elucidating the evolutionary history of maize and its relatives. Madelaine Bartlett, 2014.

10/2014 Candice Hirsch
Dyer, GA; Lopez-Feldman, A; Yunez-Naude, A; Taylor, JE. 2014. Proc Natl Acad Sci, USA. 111:14094-14099
   Genetic erosion in maize's center of origin

Crop genetic diversity is an essential resource for farmers and breeders responding to the changes in climate as well as pest and disease pressures that we are facing. Countless studies have demonstrated extensive genotypic and phenotypic diversity in maize, and much of this diversity has been captured and maintained in germplasm banks. However, unlike germplasm banks, in situ conservation allows crops to evolve in response to changing pests, diseases, and climate changes. On farm diversity in Mexico, the center of origin for maize, is an essential part of maintaining diversity that is continuously evolving in response to these changes. Average varietal richness per farm is a key statistic for in situ diversity conservation in crops. In this paper, the authors compare farm richness estimates based on cross-sectional case study data and longitudinal survey data from representative rural farms in Mexico to assess conservation. They show there has been significant decrease in maize diversity based on these metrics, and provide a social perspective to these changes. This is the first study to formally assess genetic erosion in a center of crop diversity and has significant implications surrounding conservation of maize diversity. Candice Hirsch, 2014.

10/2014 Madelaine Bartlett
Ding, Y, et al. 2014. BMC Plant Biology. 14:141
   Dehydration stress memory genes of Zea mays; comparison with Arabidopsis thaliana

In this study, the authors probe the intriguing phenomenon of "stress memory" in plants, where the first and subsequent biological responses to an abiotic stress are distinct. They compared the transcriptional response, using RNA-Seq, of maize seedlings after 1 and 3 dehydration stress-recovery events. Both maize and A. thaliana display a "memory response" to dehydration, but the character and dynamics of the response are divergent in these two species. For example, the regulation of the response appears to be divergent between the two species. Similar percentages of transcription factors were identified as "memory genes", but were enriched for very different functional classes. This study highlights the difficulty, in the study of complex phenotypic responses, of transferring information gained from one system to another over millions of years of evolution. Madelaine Bartlett, 2014

10/2014 Andrea Gallavotti
Durbak, AR et al. 2014. Plant Cell 26:2978-2995
   Transport of boron by the tassel-less1 aquaporin is critical for vegetative and reproductive development in maize

As highlighted last month, the micronutrient boron (B) is essential for plant development. In this paper, Durbak et al. isolated and characterized the tassel-less1 (tls1) mutant of maize and showed that tls1 encodes a member of the aquaporin family of channel proteins. Transport assays in frog oocytes demonstrate that TLS1 facilitates the movement of boron across the membrane. In maize, tls1 mutants display boron transport deficiencies that result in reduced levels of cross-linked rhamnogalacturonan II (RG-II), a pectin polysaccharide that is a major structural component of the cell wall and requires boron to dimerize. These deficiencies at the cell wall cause widespread developmental defects, affecting meristem and organ development, and eventually maize fertility. The authors also show that crosses between tls1 and rte, a maize mutant caused by lesions in a specific boron efflux transporter (see September review), show environmentally dependent nonallelic noncomplementation, suggesting that the two proteins function in the same pathway to facilitate transport of boron from the root to the shoot of maize plants. The transport of boron via the concerted activities of channel and transporter proteins was previously shown in Arabidopsis, suggesting that this pathway is conserved between monocots and eudicots. While a basic pathway for boron uptake from the soil has been established, is still unclear how boron is distributed in the shoot and in inflorescences, despite its importance for worldwide crop productivity. The discovery of tls1 and rte and their role in inflorescence development and reproductive success provides the first tools to investigate this process in maize. Andrea Gallavotti 2014

9/2014 Candice Hirsch
Burdo, BL, et al. 2014. Plant J. 0:doi: 10.1111/tpj.12623
   The Maize TFome - Development of a transcription factor open reading frame collection for functional genomics

Understanding the regulation of gene expression is essential in our efforts to understand plant growth and development and to be able to generate improved crop plants. Transcription factors play an essential role in regulating gene expression through the recognition of cis-regulatory elements. Determining the genes regulated by transcription factors is an intensive process that first begins with identification of the TFome. As with other omes, the TFome is defined as the collection of all (or a significant set) of the transcription factors for an organism. In this paper, the authors characterize the maize TFome and provide recombination-ready vectors consisting of 2,017 unique maize transcription factors and co-regulators. These clones provide a unique resource for functional genomics in maize. Candice Hirsch, 2014.

9/2014 Andrea Gallavotti
Chatterjee, M et al. 2014. Plant Cell 26:2962-2977
   The boron efflux transporter ROTTEN EAR is required for maize inflorescence development and fertility

In crops, proper boron nutrition is critical for obtaining high yields and high quality harvests. In maize, low levels of boron in the soil affect vegetative and in particular reproductive development, eventually causing widespread sterility in its inflorescences. This work reports the isolation and characterization of a novel maize mutant, rotten ear (rte) that shows impaired development of maize inflorescences. Positional cloning revealed that it encodes a boron efflux transporter responsible for transporting boron to the xylem. rte is co-orthologous to the Arabidopsis BOR1 gene, the first boron transporter identified in plants. RTE can rescue the developmental defects of bor1 mutants, indicating that the function of this class of transporters is conserved in monocot and eudicot species. The severity of the rte phenotype correlates with the availability of boron in the soil and can be rescued by boric acid treatments. Microscopic imaging shows that boron deficiency triggers widespread cell death in rte mutant inflorescences. In a companion paper by Durbak et al. 2014, the authors identified an additional player in maize boron uptake, the tassel-less1 gene. Together these two genes constitute a major boron transport pathway that is essential to maize inflorescence development. Check back next month for a review of this paper. Elucidating the mechanisms of boron transport and its roles in plant growth will enable the design of new strategies to alleviate deficiency or toxicity problems and increase crop production in several areas of the world. Andrea Gallavotti, 2014.

9/2014 Madelaine Bartlett
Zhang, J et al. 2014. J Exp Bot 65:5063-5076
   The ZmCLA4 gene in the qLA4-1 QTL controls leaf angle in maize (Zea mays L.)

Entrez Gene entry given (100193776) and GenBank accession (JN409349) align to la1 (lazy1)

Leaf angle is an important agronomic trait, with a complex genetic architecture. In this study, Zhang and colleagues worked to clone the gene responsible for a large leaf angle QTL, qLA4-1, responsible for 36.82% of leaf angle variance in a cross between D132 and Yu82. Fine mapping and positional cloning identified ZmLAZY1 (ZmLA1, referred to as ZmCLA4 in the manuscript) as a likely candidate gene underlying qLA4-1. The authors identified coding region SNPs between the two variants, a subset of which were associated with leaf angle variation in a panel of 75 inbred lines. qRT-PCR, RNAi lines in maize, and an overexpressor line in rice all provided evidence that higher expression levels of ZmLA1 are negatively correlated with leaf angle, and positively correlated with gravitropic response. There were also leaf-anatomical changes associated with ZmLA1 variation, but at this stage it is unclear how, exactly, this variation might impact leaf angle. All in all, this paper represents a step forward in characterizing the molecular infrastructure of phenotypic variability. Madelaine Bartlett, 2014.

8/2014 Andrea Gallavotti
Xiong, W et al. 2014. Proc Natl Acad Sci, USA 111:10263-10268
   HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

Helitrons are a rather mysterious class of transposable elements found in both plant and animal genomes. They were first identified by bioinformatics analysis in the late nineties. Helitrons comprise a unique class of transposable elements that lack terminal inverted repeats and target site duplications, are highly divergent, and whose mechanism of transposition is not yet fully understood. Nonetheless, they make up a significant amount of the DNA found in plant genomes. Helitrons have been shown to capture gene sequences and regulatory elements, and therefore have the potential to play an important role in genome evolution. In this paper, Xiong et al. developed a new tool for identifying Helitrons in plant genomes, called HelitronScanner. HelitronScanner identified more than thirty thousand new Helitrons in the maize B73 genome (6.6% of the genome) and identified Helitrons in plant species where no Helitrons had yet been reported. Compared to previously published tools, HelitronScanner is capable of detecting more divergent elements and provides a clearer representation of the Helitron content of different plant genomes. The increased number of Helitrons identified in this study helped to define a short but universal pattern shared by the majority of Helitrons that may help to shed light on the mechanism of transposition. Andrea Gallavotti 2014.

8/2014 Madelaine Bartlett
Wu, C; Diggle, Pamela; Friedman, W. 2013. Proc Natl Acad Sci, USA. 110:2217-22
   Kin recognition within a seed and the effect of genetic relatedness of an endosperm to its compatriot embryo on maize seed development

The endosperm and the embryo in angiosperm seeds are both the products of a fertilization event, but the endosperm does not pass on its genetic material. Instead, the endosperm is consumed by the embryo and the developing seedling. This role for the endosperm in development might be considered in terms of the evolutionary theory surrounding altruism, genetic conflict, and cooperation. There has been much theorizing about these ideas as they relate to angiosperm reproduction, but few experimental studies. This paper presents one such study. The authors used maize as a system to test one key prediction arising from the theory: the degree of cooperation between an endosperm and its sister embryo should be correlated with genetic relatedness. Maize exhibits a phenomenon termed heterofertilization, where the egg and the central cell can be fertilized by sperm from two different pollen tubes. Using a combination of rare heterofertilization events, divergent inbred lines, and variation at the R color locus, the authors found evidence for conflict between the embryo and the endosperm in heterofertilized kernels. Although it remains uncertain as to whether or not there is a connection between this conflict and fitness, this study presents important empirical evidence for one piece of longstanding evolutionary theory. Madelaine Bartlett, 2014.

8/2014 Candice Hirsch
Jamann, TM et al. 2014. Genetics 198:333-344
   Unraveling genomic complexity at a quantitative disease resistance locus in maize

Extensive genome-wide structural variation has been demonstrated in maize including presence/absence variation, copy number variation, and structural rearrangements. However, there are a limited number of examples where structural variants have been linked to a phenotype. One notable example in maize is the MATE1 copy number variant that is associated with aluminum tolerance (Maron et al., PNAS 2013). In this paper, the authors dissected a quantitative disease resistance locus that can condition resistance to both northern leaf blight and Stewart's wilt. The region that the two overlapping QTL mapped to showed little to no recombination suggesting possible structural variation between the parents of the mapping population. Using read depth variation as an estimate of copy number variation, the authors found large variation in read depth across the region between Tx303 and the reference genome. This data further suggests that structural variation may be important in the disease resistance at the locus. Candice Hirsch, 2014.

8/2014 Matthew Hufford
Lemmon, ZH; Doebley, JF. 2014. Genetics 198:345-353
   Genetic dissection of a genomic region with pleiotropic effects on domestication traits in maize reveals multiple linked QTL

There are currently no comments for this article.

7/2014 Madelaine Bartlett
Nestler, J et al. 2014. Plant J 79:729-740
   Roothairless5, which functions in maize (Zea mays L.) root hair initiation and elongation encodes a monocot-specific NADPH oxidase

Root hairs, which represent up to 77% of the root surface of cereals, are instrumental in plant nutrient acquisition. The molecular genetics underlying the precise patterns of root hair initiation characteristic of Arabidopsis have been fairly well characterized. In maize, however, where root hair initiation is unpredictable, the process is far less understood. Up until now only a handful of genes controlling root hair initiation and growth have been cloned. In this paper, the authors report the cloning of one more gene: roothairless5 (rth5). rth5 was identified from an EMS mutagenesis screen and produces fewer, shorter root hairs. rth5 encodes an NADPH oxidase, and may produce the ROS that trigger cell wall loosening and growth of the root hairs. Exactly how rth5 might work, as well as upstream patterning mechanisms remain elusive, but this paper represents a step forward in understanding this agronomically important aspect of plant growth and development. Madelaine Bartlett, 2014

7/2014 Matthew Hufford
Schaefer, RJ; Briskine, Roman; Springer, NM; Myers, CL. 2014. PLoS One. 9:e99193
   Discovering functional modules across diverse maize transcriptomes using COB, the co-expression browser

Transcriptome-wide studies of correlation in gene expression across samples (i.e., co-expression studies) represent a powerful and increasingly popular approach for functional characterization of specific genes and identification of candidates relevant to a trait of interest. In their recent manuscript, Schaefer and co-authors build two co-expression networks using data generated from 1) 60 different tissues/stages of the maize reference line B73 and 2) 62 diverse maize and teosinte lines. Clusters of genes within these two networks were enriched for gene ontology categories, showing clear functional coherency. Gene clusters also contained many unannotated genes allowing for putative functional characterization based on "guilt by association". The co-expression networks developed in this project have been made publicly available in COB: The Co-expression Browser ( As illustrated in two case studies presented in the manuscript, COB represents a valuable new tool for functional characterization in maize. Matthew Hufford, 2014

7/2014 Andrea Gallavotti
Li, Q; Eichten, SR; Hermanson, PJ; Springer, NM. 2014. Genetics. 196:667-676
   Inheritance patterns and stability of DNA methylation variation in maize near-isogenic lines

The regulation of gene expression by epigenetic modifications occurs in many eukaryotic organisms. DNA methylation is a major contributor to epigenetic regulation of gene expression and is established de novo by small RNAs and maintained by different methyltransferases. To better understand the frequency of epigenetic changes within a population over time as well as the inheritance of differentially methylated regions (DMRs) over multiple generations, in this study the authors analyze the inheritance of approximately 1000 DMRs from a panel of 71 near-isogenic lines (NILs) derived from B73 and Mo17 inbreds. The goal of this study was to characterize the inheritance and stability of these DMRs in the near-isogenic population. By characterizing methylation levels using an array-based approach they determined that i) in the majority of the loci, methylation level differences are stably and locally (cis) inherited across generations and do not require reprogramming by small RNAs and ii) only a few loci are influenced by other alleles or genomic regions due to paramutations or trans-acting control. Determining the stability and inheritance of epialleles in segregating as well as natural populations is crucial to our understanding of gene expression regulation, and its role in the rich phenotypic diversity observed in all species. Andrea Gallavotti 2014.

7/2014 Candice Hirsch
Li, L, et al. 2014. Genome Biol. 0:doi: 10.1186/gb-2014-15-2-r40
   Genome-wide discovery and characterization of maize long non-coding RNAs

The central dogma of "DNA makes RNA make protein" over simplifies the role of RNA in regulation of gene expression. In fact, numerous classes of non-coding RNA molecules have been defined, such as small nuclear RNAs, small nucleolar RNAs, microRNAs, small interfering RNAs, and long noncoding RNAs (lncRNAs) among others. The class of lncRNAs is defined as being greater than 200 bp in length and non-protein coding. Next generation sequencing technologies have allowed for genome-wide characterization of these lncRNAs in numerous animal and plant systems, and functional roles for lncRNAs are being discovered. In this paper, the authors surveyed all public EST and RNAseq datasets to comprehensively annotate putative lncRNAs in maize and classified them as likely small RNA precursors (18,459) and high confidence lncRNAs (1,704). Tissue specific expression was observed for 54% of the lncRNAs compared to 8% of the B73 filtered gene set based on the Shannon entropy measure of tissue-specificity. Interestingly, eQTL analysis revealed that maize lncRNAs are more affected by trans genetic factors than by cis genetic factors. This study provides a powerful tool for downstream research to characterize the functional roles of lncRNAs in maize. Candice Hirsch, 2014.

7/2014 Nancy Salazar
Hughes, TE; Langdale, JA; Kelly, S. 2014. Genome Res. 0:
   The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole genome duplication in maize

There are currently no comments for this article.

6/2014 Nancy Salazar
Yan, H et al. 2014. Biochem Biophys Res Commun 0
   Different evolutionary patterns among intronless genes in maize genome

There are currently no comments for this article.

6/2014 Andrea Gallavotti
Li, G et al. 2014. Proc Natl Acad Sci, USA. 0:doi: 10.1073/pnas.1406383111
   Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing

Endosperm is the reservoir of proteins and carbohydrates necessary for seedling growth, and in cereal crops such as maize, it provides an essential source of food worldwide. During the first few days after pollination the maize endosperm develops from a multinucleate cell into a cellularized structure, with different cell types and specialized functions: the starchy endosperm accumulates starch and proteins; the basal endosperm layer regulates nutrient transport from the maternal tissue; the aleurone produces enzymes that degrade the endosperm reserves upon germination; and the embryo surrounding region that supports embryo development. This specialized organization occurs thanks to highly regulated transcriptional and translational activities. In this paper transcriptomic analysis of the early stages of kernel and endosperm development is presented. Eight developmental time points are analyzed by RNAseq, providing a detailed picture of transcriptional activity. The onset of transcription factors (TF) expression is given particular attention. Coexpression analysis and clustering identified two groups of TF activity, one correlated to cell type differentiation, and another one correlated to the regulation of reserve accumulation in the endosperm. Validation of several of these genes by in situ hybridizations identified a series of genes with tissue specific expression patterns, including one expressed specifically in a newly identified cell type. This study provides a reliable and robust analysis of transcription in kernel and endosperm development, and together with the recently published proteome of developing seeds (Walley et al., PNAS 2013 ¿¿¿ Maize Editorial Board, February 2014), represents a significant step in deciphering the spatiotemporal programs that operate in cell differentiation and reserve accumulation during seed development. Andrea Gallavotti 2014.

6/2014 Madelaine Bartlett
John, CR; Smith-Unna, RD; Woodfield, H; Covshoff, S; Hibberd, JM. 2014. Annu Rev Plant Physiol Plant Mol Biol. 165:62-75
   Evolutionary convergence of cell-specific gene expression in independent lineages of C4 grasses

The evolution of C4 photosynthesis requires drastic changes at both the anatomical and at the molecular level. The photosynthetic apparatus needs to be compartmentalized into mesophyll vs. bundle sheath cells. C4 photosynthesis has evolved at least 20 times in the grasses, and it is unclear whether the required molecular specialization and compartmentalization was achieved through similar or divergent mechanisms each time. To begin to answer this question, the authors conducted deep-sequencing (RNA-Seq) analyses of bundle sheath and mesophyll cells from Setaria viridis and compare their data to an existing Zea mays dataset. Setaria and Zea represent two separate derivations of C4 photosynthesis. Genes recruited into the C4 photosynthetic pathway showed a high degree of convergence in terms of expression in either the bundle sheath or the mesophyll, especially when compared to other genes not involved in photosynthesis. One intriguing result was that, although multiple paralogs were available in the ancestral genomes of Setaria and Zea, all 10 of the core C4 enzymes used by both species were syntenic orthologs. A similar result was also observed for key transcription factors. This implies that the same gene copies were repeatedly and independently recruited in each of the two lineages. It will be fascinating to see if this pattern extends beyond Setaria and Zea, to other more distantly related C4 lineages. Madelaine Bartlett, 2014

6/2014 Candice Hirsch
Bi, YY, et al. 2014. BMC Genomics. 15:77
   High throughput RNA sequencing of a hybrid maize and its parents shows different mechanisms responsive to nitrogen limitation

Nitrogen is an important production input associated with high crop yields, but also with negative environmental effects and high economic costs. Additionally, corn plants do not incorporate the majority of the nitrogen that is applied in agricultural settings. Developing plants with improved nitrogen use efficiency will reduce environmental impacts and decrease production costs. In this paper, the authors used RNA-seq to evaluate the transcriptome of two inbred lines and their hybrid under nitrogen sufficient and limited conditions. The authors observed a large number of differentially expressed genes between the growth conditions within each genotypes and substantially more genes expressed under the nitrogen limiting condition. Comparisons between the three genotypes revealed different mechanisms to deal with nitrogen limiting growth conditions. However, gene expression in the hybrid more closely resembled the parental line with superior nitrogen use efficiency. This study adds to our understanding of nitrogen use efficiency, a trait with both environmental and economic importance. Candice Hirsch, 2014.

6/2014 Matthew Hufford
Sharma, A; Presting, G. 2014. Genome Biology. 0:
   Evolution of centromeric retrotransposons in grasses

Centromeric retrotransposons (CRs) are a particularly interesting class of elements due to their ability to target functional centromeres as insertion sites, a phenomenon that may be due to the paucity of genes in centromeres or perhaps because of a potential role of CRs in centromere function. In their recent manuscript, Sharma and Presting conduct a comparative genomic analysis of CRs in maize, sorghum, rice, and foxtail millet. They characterize six different subfamilies of these elements and discuss evidence for horizontal transfer of CRs across the species boundary. Horizontal transfer is supported in multiple instances by very young divergence times in CRs that post-date speciation. Potential mechanisms proposed for horizontal transfer include viruses and rare instances of pollen flow between species. These mechanisms have been observed in the grasses (pollen flow) and other systems (viral horizontal gene transfer). Additionally, the authors find evidence for recombination both within and between subfamilies of CRs. Based on their analysis, the authors propose two compelling hypotheses: 1) Horizontal transfer and recombination in CRs may allow them to circumvent transposition control mechanisms of their previous hosts; and 2) Horizontally transferred CRs may be able to seed centromere formation in their new hosts. Matthew Hufford, June 2014

5/2014 Matthew Hufford
Lang, Z et al. 2014. J Hered 105:576-582
   Defining the Role of prolamin-box binding factor1 Gene During Maize Domestication

Multiple lines of evidence have previously suggested that the prolamin-box binding factor1 (pbf1) gene was targeted by selection during the domestication of maize. This gene encodes a transcription factor that is known to control expression levels of seed storage proteins (zeins). Since maize kernels are substantially larger than teosinte kernels, pbf1 is a compelling candidate for further characterization. In their recent study, Lang and co-authors assessed kernel phenotypes, pbf1 expression, and zein protein profiles in near-isogenic lines (NILs) with both maize and teosinte alleles at the pbf1 locus. Surprisingly, the authors found two-fold higher expression and larger and heavier kernels in plants with the teosinte allele rather than the maize allele. The authors also could not detect expression-level differences in known targets of pbf1 and no differences in zein profiles could be attributed to the presence of a teosinte versus maize allele. A number of potential confounding factors and explanations for these largely negative results were mentioned including environmental effects and the influence of a mostly maize background in the NILs on domestication differences due to pbf1. The authors concluded by cautioning that the identification of phenotypes altered by domestication can be quite challenging, even when the candidate under consideration has a well-known biological function. Matthew Hufford, 2014

5/2014 Candice Hirsch
Martin, JA, et al. 2014. 4:DOI: 10.1038/srep04519
   A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing

Next generation sequencing has expanded the breadth and depth of questions that biologist are now able to ask. Next generation sequencing has already been used to study the genome, transcriptome, and epigenome of maize and other species. However, as with any technology, it is important to understand both the benefits and limitations of next generation sequencing approaches. In this paper, the authors address an important question relating to consequences of sequencing depth with regards to RNA sequencing (RNA-seq) using extremely deep sequencing of the B73 seedling transcriptome. Among the findings in this paper, the authors show that relative to simulated "shallow sequencing" (20 million reads), they were able to detected on average 7,444 more 5b transcripts, and showed that many of the missed transcripts were associated with transcription factor activities. They were also able to improve the current B73 structural annotation including expanding gene models and identifying unannotated genes. This manuscript provides important insights on sequence depth considerations, which in part depends on the scientific goals of that study. Candice Hirsch, 2014.

5/2014 Nancy Salazar
Luan, M et al. 2014. PLoS One 9:e91369
   Family-wide survey of miR169s and NF-YAs and their expression profiles response to abiotic stress in maize roots

There are currently no comments for this article.

5/2014 Madelaine Bartlett
Kim, H, Kim, JS, 2014. Nat Rev Genet 15:321-34
   A guide to genome engineering with programmable nucleases

Targeted genome editing using programmable nucleases has great potential as a tool for geneticists of all flavors. There are three main types of programmable nucleases that might be of utility in probing gene function: zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and RNA-guided engineered nucleases (RGENs). RGENs, in particular, have been the subject of much discussion in the plant community recently, as part of the CRISPR/Cas9 system (Clustered Regular Interspaced Short Palindromic Repeat/CRISPR-associated protein 9). Although not focused on their use in plants, this paper offers a timely review of all three systems: how they work, and each of their pros and cons. Madelaine Bartlett, 2014.

5/2014 Andrea Gallavotti
Rice, EA; et al. 2014. PLoS One. 9:e94238
   Expression of a Truncated ATHB17 Protein in Maize Increases Ear Weight at Silking

The dynamic regulation of transcription is essential for every aspect of plant growth. This is generally accomplished by both transcriptional activation and repression mechanisms. Recent evidence suggests that transcriptional repression is a common and widespread regulatory mechanism employed by many developmental and hormonal pathways. The homeodomain leucine zipper II (HD-Zip II) family of transcription factors is a large family whose members are known to homo and heterodimerize and to regulate an array of pathways. The Arabidopsis ATHB17 protein carries a well-known repressor motif (EAR motif) that confers transcriptional repression ability when tested in a protoplast-based repression assay. In this study the full-length HD-Zip II gene ATHB17 gene was overexpressed in maize, but it was soon noted that a truncated version of the protein lacking the EAR motif was produced. Since this truncated version retained the ability to homo and heterodimerize as well as bind DNA, it prompted the authors to investigate if it could act as a dominant negative to endogenous maize HD-Zip II proteins. By using the protoplast repression assay the authors showed that by adding increasing concentration of the truncated ATHB17 expression construct they were capable of decreasing the repressor ability of maize HD-Zip II proteins. Finally, the authors analyzed the phenotype of maize transgenic lines expressing the dominant negative version of the Arabidopsis ATHB17 and discovered an increase in ear weight without concurrent increase in vegetative biomass in replicated field plots. Analysis of the transcriptome of these lines revealed only subtle changes in global transcript levels in ears. Overall, these results show the importance of studying the mechanisms of transcriptional regulation in plants, a knowledge that can provide new molecular tools to improve crop performance by modulating transcription. Andrea Gallavotti, 2014.

4/2014 Nancy Salazar
Zhang, H et al. 2014. J Integr Plant Biol 56:262-70
   Meta-analysis and candidate gene mining of low-phosphorus tolerance in maize

Breeding crop cultivars that could uptake and use soil phosphorus (P) more efficiently is critical for alleviating phosphate waste and increasing resource use efficiency in agriculture. Understanding of genetic mechanisms of low-P tolerance can help to develop low-P tolerant cultivars. The authors are focused to discover information that is important for genetics and molecular breeding of low-P tolerance in maize through meta-analysis and candidate gene mining using all QTL and molecular information currently available. Meta-analysis is an important tool for integration information from multiple quantitative trait loci (QTLs) studies from independent genetic mapping activities, which allows greater statistical power for QTL detection and more precise estimation of their genetic effects. The consensus QTL (cQTL) identified by QTL meta-analysis could delimit the QTL confidence interval and decrease the number of candidate genes. The authors identified 23 cQTL, representing 131 original QTLs using Biomercator 2.1 software and IBM2 2008 Neighbors map as the reference map, all the QTL from original maps were projected onto this map, forming QTL clusters. Among the cQTLs, 9 containing 22 genes, which are homologous to 14 genes collected from Arabidopsis, rice and white lupin. The homologs of the 22 genes in the cQTL regions are OsMYB2P-1, AtPht1;1, LaGPX-PDE2, OsPSTOL1, AtMYB2, AtLPR1, AtPHO1, miR399h, miR399i, AtSUC2, AtPht2;1, AtMGD2, AtWRKY75, AtPAH1 and AtPAP10; which were functionally characterized to influence plant low-P tolerance, and could be candidates of gene mining with possible roles in maize low-P tolerance. This study has narrowed each of 19 cQTL to less than a 10Mb interval and 4 cQTL to less than 1 Mb, that can be used for candidate locus association mapping. Miriam Salazar, 2014.

4/2014 Andrea Gallavotti
Sutimantanapi, D et al. 2014. Plant Physiol 164:1905-1917
   Divergent roles for maize PAN1 and PAN2 receptor-like proteins in cytokinesis and cell morphogenesis

Leucine-rich receptor-like proteins belong to a large gene family in plants and are used in many developmental pathways to activate downstream signaling cascades. Whereas the majority of these proteins have an active kinase domain (leucine-rich receptor-like kinases or LRR-RLKs), others lack kinase activity and are thought to function via interaction with active kinases. The maize PAN1 and PAN2 proteins belong to the latter category of LRR-like proteins and were originally identified for their function in guiding asymmetric cell divisions during stomata development. It was previously reported that PAN1 functions with Type I ROP GTPases, well known to regulate actin polymerization, and that PAN2 functions upstream of PAN1 in regulating cell polarity. In this report the authors investigate whether PAN1 and PAN2 play additional roles in other cellular processes since their expression is observed in different tissue types with actively dividing cells. This work shows that PAN1 and PAN2 have indeed additional distinct roles in cells. In particular, PAN2 is involved in regulating cell shape by affecting the accumulation of actin in a manner that is independent of PAN1 and Type I ROP GTPases, and PAN1 on the other hand participates in the development of the cell plate, the new cell wall that separates daughter cells, and acts independently of PAN2 in this process. Although the mechanisms remain to be elucidated, the authors propose that PAN proteins function either directly or indirectly via actin polymerization in all cellular contexts. Andrea Gallavotti, 2014.

4/2014 Madelaine Bartlett
O'Connor, D, et al. 2014. PLoS Comput Biol. 10:e1003447
   A division in PIN-mediated auxin patterning during organ initiation in grasses

Auxin is a key player in plant morphogenesis: the hormone has been implicated in almost every aspect of patterning. For example, directional auxin transport is known to play an important role in patterning plant vasculature and organ positioning. Competing models have arisen, all trying to explain how the auxin efflux transporter PIN-FORMED1 (PIN1) of Arabidopsis thaliana works to concentrate auxin into maxima necessary for organ initiation, and also create the narrow auxin flows necessary for vein formation. This new paper adds to the debate by investigating the PIN1-like proteins in Brachypodium distachyon. The authors identified three PIN1-like genes in B. distachyon: PIN1a, PIN1b, and Sister-of-PIN1 (SoPIN1). PIN1a and PIN1b appear to be the products of a grass-specific gene duplication. Intriguingly, SoPIN1 was found in all sampled angiosperms except for Brassicaceae family members. SoPIN1 seems to have been lost somewhere along the lineage leading to Arabidopsis and the broader Brassicaceae. Fluorescent protein fusion lines were used to follow auxin (by DR5 proxy) and the expression of all three transporters in developing B. distachyon inflorescences. The protein and auxin localization patterns suggest clear distinctions between the three proteins¿¿¿ roles: SoPIN1 creates an auxin maximum, PIN1b directs developing veins to older auxin sinks, and PIN1a refines auxin flow to a narrow vascular stream. Immunolocalization experiments suggest a similar mechanism in maize. Although there are no functional data in the grasses to support the authors¿¿¿ hypotheses, a computational model they developed reproduces their experimental observations. The results reported in this paper offer a compelling argument for investigating both auxin and PIN dynamics in a range of angiosperm taxa. Madelaine Bartlett, 2014

4/2014 Matthew Hufford
Gassmann, AJ; et al. 2014. Proc Natl Acad Sci, USA. :
   Field-evolved resistance by western corn rootworm to multiple Bacillus thuringiensis toxins in transgenic maize

Over the past few decades, the cultivation of transgenic maize producing insecticides derived from Bacillus thuringiensis (Bt) has become a widespread pest-management strategy in the American Corn Belt. This strategy has proven successful in managing western corn rootworm, a major pest of maize. In their recent manuscript, Gassmann and co-authors describe the development of resistance of western corn rootworm in Iowa to two similar Bt toxins expressed in transgenic maize, Cry3Bb1 and mCry3A. Resistant populations were found in an increasing number of fields during the period from 2009-2011 suggesting either spread of resistant individuals or multiple instances of resistance evolving. Cross-resistance was also documented, i.e., rootworms were resistant to both Bt toxins. Resistance arose rapidly over a period of less than four years of exposure to these Bt toxins, a phenomenon attributed to the low dose of these toxins expressed in maize lines. While the authors confirmed that another Bt toxin (Cry34/35Ab1) is still effective in controlling western corn rootworm, this study begs caution in managing pest resistance to transgenic crops. Refuge strategies and additional integrated pest management will likely prove essential in delaying pest resistance. Matthew Hufford, 2014.

4/2014 Candice Hirsch
Lamkey, CM; Lorenz, AJ. 2014. Crop Sci. 54:576-585
   Relative Effect of Drift and Selection in Diverging Populations within a Reciprocal Recurrent Selection Program

Maize hybrid breeding benefits greatly from heterotic pools that generate superior hybrids when inbred lines from opposite heterotic pools are crossed. The initial formation of heterotic pools in North American germplasm is a fascinating story (see Tracy and Chandler, Plant Breeding: The Arnel R. Hallauer International Symposium, 2006). Overtime, genetic divergence has occurred between the heterotic groups. Likewise, recurrent selection programs show similar genetic divergence overtime. However, it is not clear if this divergence is the result of section or random genetic drift. At the University of Nebraska, a replicated recurrent selection program was performed that allowed the authors of this study to address the question of the role of selection and drift in the establishment of strong heterotic patterns. Results of this study demonstrate the importance of genetic drift for population differentiation during reciprocal recurrent selection and possibly in shaping population structure of North American maize. Candice Hirsch, 2014

3/2014 Andrea Gallavotti
Lituiev, DS et al. 2013. Annual Review of Cell and Developmental Biology 140:4544-53
   Theoretical and experimental evidence indicates that there is no detectable auxin gradient in the angiosperm female gametophyte

The female gametophyte of most flowering plants is composed of four types of cells: synergid, egg, central and antipodal cells. It was previously proposed that fate specification of these cells is determined by an auxin gradient oriented along the micropylar to chalazal axis inside the female gametophyte that behaves in a morphogen-like manner. The formation of auxin gradients has recently been implicated in many developmental processes. In this report the authors employ mathematical models to explain the formation of the proposed auxin gradient in the female gametophyte, but determined that only shallow gradients could be achieved. In their models the authors took into account various parameters such as auxin efflux and influx, localized auxin biosynthesis and degradation, as well as the presence of the large vacuole that forms inside the female gametophyte. The theoretical gradients achieved in all conditions were determined to be too shallow to withstand small perturbations inherent to biological systems and therefore unlikely to provide the robust positional information for cell fate specification in the female gametophyte. By using in vivo imaging of fluorescent reporters for auxin response in both maize and Arabidopsis ovules, the authors show that auxin responses are not detected in the female gametophyte but rather in the surrounding sporophytic tissue. Based on these results they propose that the effect of auxin in providing positional information for cell fate specification in the female gametophyte of flowering plant is likely indirect. Andrea Gallavotti, 2014.

3/2014 Nancy Salazar
Bolduc, N; Tyers, RG; Freeling, M; Hake, S. 2014. Plant Physiol. 164:229-238
   Unequal redundancy in maize knotted1 homeobox genes

Class I knox transcription factors represent a gene family expressed in meristems and excluded from leaves. In this work the authors elucidated in maize, the role of the class I Knox gene rough sheath1 (rs1), which is only revealed in the complete absence of Knotted1 (kn1), the founding member of knox gene family. When kn1 is missing, absence of rs1 has an impact in shoot phenotype showing a limited shoots and reduced tassel branch number; otherwise kn1 will compensate for the loss of rs1 function. In contrast, rs1 cannot substitute for kn1 in kn1 mutant. In rice, similar unequal redundancy is observed between kn1 and osh1 homeobox genes in the maintenance of the shoot apical meristem. Here, the authors conclude that the knox hierarchy is conserved between rice and maize, in the orthologous pairs kn1-osh1 and kn1-rs1. In addition, the authors show that while KN1 and RS1 are both necessary for shoot development in the inbred lines B73 and Mo17, rs1;kn1 double mutants recover when not fully introgressed into B73, suggesting the possible action of modifier loci highlighting the possibility of another players in meristem maintenance. Miriam Salazar, 2014.

3/2014 Candice Hirsch
Hirsch, CN et al. 2014. Plant Cell 26:121-135
   Insights into the maize pan-genome and pan-transcriptome

Genomes at the species level are dynamic, with genes present in all individuals (core) or only in a subset of individuals (dispensable). Collectively the core and dispensable genome comprise the species pan-genome. In bacteria, it is thought that dispensable genes contribute to diversity and adaptation, and much of the early work to characterize species level pan-genomes was conducted in bacteria. More recently, pan-genome studies have been conducted at various levels in plant and animal systems. In this paper, we used transcriptome sequencing as a proxy for genome sequences to explore the maize pan genome across 503 diverse maize inbred lines. We identified nearly 9,000 novel representative transcript assemblies. Additionally, using linkage disequilibrium mapping and syntenic analysis were able to place nearly a third of these novel transcripts on the B73 genome assembly. Using SNP and expression variants in the maize pan genome, genome-wide association studies revealed loci associated with the timing of the juvenile to adult vegetative and vegetative to reproductive developmental transitions, two traits important for fitness and adaptation. This manuscript greatly expands on our understanding of the dynamic nature of the maize pan genome and the contribution of various levels of diversity to adaptive traits. Candice Hirsch, 2014

3/2014 Madelaine Bartlett
Tanaka, S et al. 2014. Elife 3:e01355
   A secreted Ustilago maydis effector promotes virulence by targeting anthocyanin biosynthesis in maize

Interactions between plants and their pathogens are mediated in part by effector proteins produced by the pathogen. Ustilago maydis (corn smut) is a biotrophic fungal pathogen of maize. U. maydis infection causes both the development of tumors and anthocyanin accumulation in infected tissues. U. maydis produces hundreds of effector proteins, the function of most of which remains unknown. In this paper, the authors elucidate the function of one U. maydis effector, Tin2. The authors show that Tin2 is a secreted protein that stabilizes a maize protein kinase, ZmTTK1, by binding to a ubiquitin-proteosome degradation motif in ZmTTK1. The stabilization of ZmTTK1 results in increased anthocyanin biosynthesis, possibly because of phosphorylation of the transcription factor R1, allowing R1 to enter the nucleus and upregulate anthocyanin biosynthesis. The authors devise an interesting model where this upregulation of anthocyanin biosynthesis diverts metabolic precursors from the lignin biosynthetic pathway. Reduced lignin biosynthesis may result in plant cells more susceptible to fungal infection, thus increasing pathogen virulence. This model is supported by analyses of U. maydis pathogenicity in biosynthetic mutants of maize. U. maydis pathogenicity was attenuated when the biosynthetic pathway to anthocyanins was blocked in chalcone synthase (c2) mutants. Lignin-affected brown midrib (bm) mutants showed U. maydis hypersensitivity. Anthocyanin accumulation is not unique to the U. maydis-maize pathogen/plant interaction. The authors may have uncovered a host metabolic rewiring strategy common to a number of plant pathogens. Madelaine Bartlett, 2014.

3/2014 Matthew Hufford
Piperno, DR; Holst, I; Winter, K; McMillan, O. 2014. Quaternary International. 0:ePub ahead of print
   Teosinte before domestication: Experimental study of growth and phenotypic variability in Late Pleistocene and early Holocene environments

Domestication of several crops around the world, including maize, occurred approximately 10,000-12,000 years ago. Environmental conditions at this time differed dramatically from current conditions; for example, carbon dioxide, temperature, and precipitation levels were all considerably lower in the New World tropics where maize was domesticated. In their recent manuscript, Dolores Piperno and co-authors report their investigation of phenotypic plasticity in the wild ancestor of maize (Zea mays ssp. parviglumis; hereafter, parviglumis) grown in chambers under current environmental conditions and those approximating the time of domestication (low carbon dioxide and temperature). Multiple parviglumis plants grown under domestication conditions were characterized by maize-like phenotypes, having few lateral branches tipped with female inflorescences, whereas all parviglumis plants in current conditions were more typical of wild Zea with multiple lateral branches tipped with tassels. The authors also observed a marked reduction in productivity of parviglumis grown in conditions during the timeframe of domestication. The remarkable, environmentally mediated phenotypic plasticity observed here suggests parviglumis encountered by early foragers and cultivators may have more closely resembled modern maize. Questions remain as to whether early cultivators' selection on these plastic responses could have led to a genetic underpinning and canalization of domestication traits. Matthew Hufford, 2014.

2/2014 Nancy Salazar
Bolduc, N; Tyers, RG; Freeling, M; Hake, S. 2014. Plant Physiol. 164:229-238
   Unequal redundancy in maize knotted1 homeobox genes

Class I knox transcription factors represent a gene family expressed in meristems and excluded from leaves. In this work the authors elucidated in maize, the role of the class I Knox gene rough sheath1 (rs1), which is only revealed in the complete absence of Knotted1 (kn1), the founding member of knox gene family. When kn1 is missing, absence of rs1 has an impact in shoot phenotype showing a limited shoots and reduced tassel branch number; otherwise kn1 will compensate for the loss of rs1 function. In contrast, rs1 cannot substitute for kn1 in kn1 mutant. In rice, similar unequal redundancy is observed between kn1 and osh1 homeobox genes in the maintenance of the shoot apical meristem. Here, the authors conclude that the knox hierarchy is conserved between rice and maize, in the orthologous pairs kn1-osh1 and kn1-rs1. In addition, the authors show that while KN1 and RS1 are both necessary for shoot development in the inbred lines B73 and Mo17, rs1;kn1 double mutants recover when not fully introgressed into B73, suggesting the possible action of modifier loci highlighting the possibility of another players in meristem maintenance. Miriam Salazar, 2014.

2/2014 Matthew Hufford
Mezmouk, S; Ross-Ibarra, J. 2014. G3 4:163-171
   The pattern and distribution of deleterious mutations in maize

Most newly arising mutations are thought to be deleterious and should be kept at low frequency, particularly when their negative effects on fitness are strong. Despite their rarity, deleterious mutations are believed to play an important role in disease and variation in quantitative traits and may, through the process of complementation, underlie hybrid vigor observed in crosses between heterotic groups of maize. In their recent study, Mezmouk and Ross-Ibarra conduct a genome-wide analysis of putatively deleterious mutations across a panel of 247 maize inbred lines. Using prediction software to gauge the effects of amino acid changes, the authors estimate that 20-40% of coding SNPs have a deleterious allele segregating in their sample. Based on analysis of phenotypic data from their panel, the authors find that genes containing deleterious mutations are more likely to be associated with hybrid vigor. This latter result provides compelling evidence consistent with the dominance hypothesis of heterosis; deleterious mutations in one heterotic group may be complemented by an alternative allele in another. In addition, while previous work has suggested elevated residual heterozygosity in pericentromeres may be caused by inefficient selection in these regions due to their low recombination rate, Mezmouk and Ross-Ibarra find no enrichment of deleterious mutations in pericentromeres suggesting there is enough recombination over the long-term for their removal through selection. Matthew Hufford, 2014.

2/2014 Madelaine Bartlett
Waters, AJ. et al. 2013. Proc Natl Acad Sci, USA 110:19639-19644
   Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species

Imprinting, the differential expression of maternally- and paternally-derived alleles, was initially described in maize, but has also been described (and studied) in mammals. Imprinting is particularly interesting to students of epigenetic reprogramming, and those considering theories of genetic conflict. In plants, the endosperm is the main site of imprinting. Until the advent of next-generation sequencing techniques like deep sequencing of RNA (RNA-Seq), only a handful of imprinted genes had been identified. This new paper represents a comprehensive analysis of imprinting in maize, across four divergent maize genotypes. The experimental design allowed the identification of both maternally and paternally expressed genes (MEGs and PEGs), as well as genes that showed allelic variation for imprinting. One observation the authors make is that MEGs and PEGs are usually treated as a single class, but their analyses reveal a few distinctions. For example, MEGs are far more likely to be endosperm-specific in their expression, while PEGs are more often associated with H3K27me3. In line with previous investigations, very little overlap in imprinted genes was discovered both between maize genotypes, and between maize and rice. Those genes that were identified as conserved within and between species, however, represent an interesting set of targets to pursue in studies of gene function. Madelaine Bartlett, 2014.

2/2014 Candice Hirsch
Walley, JW, et al. 2013. Proc Natl Acad Sci, USA. 110:E4808-17
   Reconstruction of protein networks from an atlas of maize seed proteotypes

Genome-wide atlases of gene expression have been generated in many plant species, including maize (see Sekhon et al, The Plant Journal, 2011). These large datasets can provide valuable insights into expression patterns among tissues and organs as well as expression throughout the course of development, and are extremely useful in addressing an array of biological questions. Often, measures of transcript abundance are used to infer the proteome of a cell, tissue, or organ. However, in this paper, the authors took on the major task of generating a quantitative atlas of proteotypes from different seed components throughout development using mass spectrometry. Interestingly, the authors also demonstrated poor correlation between mRNA levels and protein abundance. Because of the quantitative nature of the data, the authors were able to reconstruct biochemical and signaling networks important for seed development and the production of seed storage products and provide valuable new insights into seed development. Candice Hirsch, 2014.

2/2014 Andrea Gallavotti
Eveland, AL, et al. 2013. Genome Res. 0:DOI: 10.1101/gr.166397.113
   Regulatory modules controlling maize inflorescence architecture

Meristem activity shapes the architecture of plant inflorescences and is responsible for the vast diversity of reproductive structures found in nature. Meristems can have a determinate or indeterminate fate. In the former case they terminate in a differentiated structure, such as a flower, whereas in the latter case they prolong their activity and form branches. In maize, the ramosa mutants (ramosa1, ramosa2, ramosa3) are all characterized by a loss of meristem determinacy and as a result ears and tassels show various degrees of branching. In this report, Eveland et al. employed the ramosa mutants as tools in a series of genomic approaches aimed at understanding the regulation of meristem determinacy. Using a combination of RNA-seq analysis of all three mutants and ChIP-seq of the zing-finger transcription factor RAMOSA1, this report identifies genome-wide targets of RA1 activity, defines its binding sites and provides evidence for both positive and negative regulation of downstream transcriptional targets. Interactions with previously known factors regulating inflorescence architecture, such as liguleless1 and knotted1, are described. Overall, this report provides detailed expression profiling of the early stages of ear and tassel development and identifies regulatory networks involved in meristem activity. Andrea Gallavotti, 2014.

1/2014 Madelaine Bartlett
Moon, J et al. 2013. Plant J 76:592-602
   Regulation of cell divisions and differentiation by MALE STERILITY32 is required for anther development in maize

Maize anthers, and indeed those of all angiosperms, contain a series of clearly defined cell types and cell layers. This paper provides new insight into the genetic regulation of the development of these cell layers. The male sterile 32 (ms32) mutant exhibits extra cell layers, that fail to differentiate as expected (the tapetum fails to differentiate). Pollen mother cells are squashed by the extra somatic cell layers and fail to go through meiotic prophase one, resulting in male sterile plants. ms32 encodes a bHLH transcription factor expressed specifically in pre-meiotic anthers. ms32 is the ortholog of the rice gene UNDEVELOPED TAPETUM1 (UDT1), but the mutant phenotypes in rice and maize are distinct (although background effects were not investigated). Apart from identifying one more genetic player in the development of anthers, this study presents an interesting example of divergent functions of orthologous genes in fairly closely related species, in a process one would think would be highly conserved in flowering plants as a whole. Madelaine Bartlett 2014.

1/2014 Nancy Salazar
Garsmeur, O, et al. 2013. Mol Biol Evol. 0:doi: 10.1093/molbev/mst230
   Two evolutionarily distinct classes of paleopolyploidy

It has been described previously that two sub-genomes can be identified in maize, the result of an ancestral whole genome duplication (WGD) event. The two sub-genomes differ in dominance and exhibit biased fractionation (the process of gene loss following WGD), which suggests questions about the retention of duplicated gene pairs. In this paper, the authors propose a generalized fractionation-dominance model, where bias in gene expression is responsible for bias in gene loss within the genome. Based on sub-genome behaviour, the authors recognize two classes of WGD event: Class I, in which one sub-genome shows a higher level of gene expression than the other, and an associated greater rate of gene retention; Class II, in which sub-genomes show equal gene expression, associated with unbiased fractionation. The authors propose that Class I is associated with ancient allotetraploidies, while Class II is associated with ancient autotetraploidies. Their analysis of gene deletion and gene expression in maize, positions it within Class I. Miriam Salazar, 2014

1/2014 Candice Hirsch
Romay, MC et al. 2013. Genome Biology 14:R55
   Comprehensive genotyping of the USA national maize inbred seed bank

Characterizing genetic diversity and the genetic architecture of phenotypic traits is important for addressing issues related to sustainable agriculture and climate change. The body of literature on the role of rare allelic variants in phenotypic diversity is growing rapidly. Identifying rare variants through GWAS is difficult and requires large sample sizes. GWAS studies in maize to date have used relatively small diversity panels, and as such do not represent the breadth of rare variants in maize. In this paper, the authors genotyped the entire USA national maize inbred seed bank, which contains 2,815 inbred accessions from breeding programs all over the world. Of the nearly 700K identified single nucleotide polymorphisms (SNPs), nearly half were rare in the collection. Additionally, the data set showed that, while much of the available diversity has been incorporated into public temperate breeding programs, only a modest amount is present in commercial germplasm. The utility of this data set for performing genome-wide association studies (GWAS) was tested. While associations were identified for SNPs near candidate genes, the authors suggest that even higher SNP density may be needed to fully characterize the genetic architecture of complex quantitative traits. Candice Hirsch, 2014.

1/2014 Andrea Gallavotti
Bommert, P et al. 2013. Nature 502:555-558
   The maize Gα gene COMPACT PLANT2 functions in CLAVATA signalling to control shoot meristem size

Meristems are small group of stem cells responsible for post-embryonic plant development. Throughout development meristems need to constantly create new organs at their flanks as well as maintain their core stem cell niche to avoid termination. In some species, meristems are maintained for decades. A well-established pathway for meristem maintenance is the WUSCHEL-CLAVATA (WUS/CLV) negative feedback loop, first identified in Arabidopsis based on analysis of mutants defective in shoot apical meristem maintenance. In maize, a similar pathway exists and members of this pathway have been isolated throughout the years by studying mutants with fasciated inflorescences. This new report by Bommert et al. identifies a previously undiscovered player in this pathway, COMPACT PLANT2 (CT2) that encodes the G-alpha subunit of a heterotrimeric GTP binding protein. Heterotrimeric G proteins are well-known secondary messengers that link signals emanating from seven-pass transmembrane G-protein coupled receptors to various intracellular effectors. In this paper, CT2 is shown to genetically and physically interact with the LRR-receptor like protein FEA2/CLV2, suggesting that CT2 is part of the signaling pathway that controls meristem size and challenging the common belief based on studies in yeast and animal systems that G-alpha proteins only interact with seven-pass transmembrane G-protein coupled receptors. This discovery may explain how LRR-receptor like proteins, such as FEA2/CLV2 that lack a kinase domain, can transmit an intracellular downstream signal. Finally, this report represents another nice example of the importance of using different model systems to dissect complex developmental pathways. Andrea Gallavotti, 2014.

1/2014 Matthew Hufford
Wang, K et al. 2013. Genome Res pp.doi:10.1101/gr.160887.113
   Maize centromeres expand and adopt a uniform size in the genetic background of oat

While centromeres, as assembly sites for kinetochores responsible for chromosomal segregation, serve an essential function, their position along a chromosome is somewhat labile. In this investigation, Wang and co-authors characterize centromere lability in nine oat-maize addition lines in which a single maize chromosome has been introduced into an oat background. Previous work had shown that total centromere area is correlated with genome size. The genome of oat is roughly four times the size of maize with oat having only twice the number of chromosomes. The authors therefore hypothesize that maize centromeres in oat-maize addition lines should double in size. Using chromatin immunoprecipitation for the centromeric histone CenH3, the authors measure maize centromere size in addition lines and find their hypothesis to be well supported; while the average maize centromere in its native context is 1.8 Mb, the centromeres of maize chromosomes in oat-maize addition lines is closer to 3.6 Mb, stretching into gene-poor regions. Moreover, two addition lines containing maize chromosome 3 show formation of neocentromeres in which the original position of the maize centromere has changed entirely. In both cases, neocentromeres form in gene-poor regions with the majority of genes in these regions not being expressed. The findings of Wang and co-authors importantly suggest that, despite lability in centromere position, constraints of genome size and gene density determine the area occupied by centromeres. Matthew Hufford, 2014

12/2013 Lewis Lukens
McCarty, DR, et al. 2013. PLoS One. 8:e77172
   Mu-seq: Sequence-based mapping and identification of transposon induced mutations

Insertional mutagenesis with the Robertson's Mutator transposon has been important for both forward and reverse genetics in maize. The availability of a large collection of lines with insertions within many different genes is a key resource for gene function investigations. Families within the Uniform-MU population contain novel and stable Mu transposon insertions. There are currently over 45,500 germinal Mu insertions in over 8,236 maize lines. In this report, McCarty et al. describe a novel method for identifying Mu insertions within Uniform-MU families using targeted high-throughput sequencing. They start by assigning each of 576 families a position on a 24 x 24 grid. They extract two DNA samples on the opposite sides of plants from the 576 families. One DNA sample is pooled with a set of 23 families along a grid row, and the other DNA sample is pooled with a set of 23 families along the column. An analysis of Mu insertions within the 24 row and 24 column samples can identify the precise family in which an insertion has occurred by using the intersection of the two axes in which an insertion is detected. A problem with this approach is that Mu elements are numerous within the maize genome, and it can be tricky to identify novel insertions among ancestral insertions. Here, McCarty et al. selectively amplify flanking sequence from only the terminal inverted repeats of Mutator transposons that are most active in plants with autonomous MuDR elements. With about 100 million 100 bp sequence reads, McCarty et al.'s method identifies 4,723 novel, germinal transposon insertions- insertions detected both in one column sample and in one row sample. The method distinguishes distinct Mu insertions at the same locus when the insertion sites differ by as little as a single nucleotide. Interestingly, 13,218 insertions have substantial sequence support but were found in a single column or row sample, suggesting somatic insertions of Mu. These single axis reads are greatly over-represented in certain samples suggesting that about 1% of the families have Mu activity. Mu activity remains despite selection against activity based on bz1-mum9 expression, perhaps because of epigenetic phenomena. Lewis Lukens 2013

12/2013 Ruairidh Sawers
Lu, Y et al. 2014. Plant Reproduction 27:19-20
   Genetic and cellular analysis of cross-incompatibility in Zea mays

In Mexico, the ancestral home of maize, there is great interest in gene flow among populations of ancestral teosinte, landrace maize, and imported hybrid varieties. Here, Lu and colleagues remind us that, in addition to ecological factors and cultural practice, plant biology plays a key role also in this process. Three genetic systems have been well described that confer cross-incompatibility between domesticated maize and wild teosinte. While the molecular mechanisms underlying these systems remain elusive, Lu and colleagues provide further data that extend our knowledge of the genetic basis of the Teosinte crossing barrier1 (Tcb1) locus. Cross-incompatibility barriers consist of two functions, female and male: the female function confers the silk-barrier to incompatible pollen; the male function determines the competence of pollen to fertilize silks expressing the female function. While a rare haplotype that confers male function only has been identified in natural teosinte populations, Lu and colleagues, through detailed analysis of recombinants, separate genetically the female and male functions of a Tcb1, suggesting a possible complex locus. Further, the authors characterize arrest of pollen-tube growth in incompatible interactions. Intriguingly, the morphology of arrested pollen-tubes is different between Tcb1 and other known cross-incompatibility systems, suggesting that various mechanisms may be involved. Finally, the authors report the loss of cross-incompatibility in lineages carrying active Mutator transposons. The potential availability of transposon-tagged alleles of Tbc1 has clear implications to the molecular identification of the gene or genes that constitute the Tbc1 locus. As the authors point out, cloning of the genes involved will go a long way to finally untangling the history and mechanism of one of the great stories of maize population biology. Ruairidh Sawers, 2013